All surgery requires the set of medical tools in the Operating Theatre, along with a table (a surgical table gives no negative results). For the most part, only medical doctors and the Chief Medical Officer can perform advanced surgery.
Surgical Tools
Information about every tool used in surgery can be found here.
Surgical Procedures
Eye Surgery
Fixing blindness.
Step 1: 
Place the patient onto the operating table.
Step 1.5: 
Use a tank of anesthetic and a breath mask to make your patient sleep. (Optional)
Step 2: 
Place drapes over the patient's eyes.
Step 3: 
Aim for the patient's eyes, and cut the skin around them with your scalpel.
Step 4: 
Use your retractor to lift up the eyes.
Step 5: 
Use your hemostat to stop any potential bleeding.
Step 6: Use hemostat again to fix the patient's eyes.
Step 7: 
Use your cautery to seal the wound.
Step 8: Wake up your patient, congratulate them on their new vision.
Brain Surgery
The nerds next door may be doing rocket science, but hey, it's not exactly brain surgery.
Step 1: Place the patient onto the operating table.
Step 1.5: Use a tank of anesthetic and a breath mask to make your patient sleep. (Optional)
Step 2: Place drapes over the patient's head.
Step 3: Aim for the patient's head with your scalpel to cut back the flesh.
Step 4: Clamp bleeders with the hemostat (or use wirecutters).
Step 5: Retract tissue with retractor.
Step 6: 
Cut through the skull with your saw.
Step 7: Extract the brain with the hemostat (or use a crowbar).
Step 8: 
Deal with the brain, typically by putting it in an MMI and then giving it to a roboticist.
Step 9: 
Morgue the body.
Putting a brain back in:
Step 1: Place the patient onto the operating table.
Step 2: 
Cram their brain back into their skull.
Step 3: 
Usually, you take the body to be cloned.
Xenomorph Brain Surgery
Step 1: Place the patient onto the operating table.
Step 1.5: Use a tank of anesthetic and a breath mask to make your patient sleep. (Optional) Anesthetic cannot be used on Xenomorphs. Enjoy their screams of pain.
Step 2: Place drapes over the patient's head.
Step 3: Cut through the skull with your saw.
Step 4: Aim for the patient's head with your scalpel to cut back the flesh.
Step 5: Retract tissue with retractor.
Step 6: Cut through the skull with your saw.
Step 7: Extract the brain with the hemostat (or use a crowbar).
Step 8: 
Deal with the brain, typically by putting it in an MMI and then giving it to a roboticist. Alternatively, let genetics make a new person from the brain to fight the alien horde.
Step 9: Morgue the body. The chef might also like the body to make some tasty Xeno Burgers.
Implant Removal
Step 1: Place the patient onto the operating table.
Step 1.5: Use a tank of anesthetic and a breath mask to make your patient sleep. (Optional)
Step 2: Place drapes over patient's chest.
Step 3: Aim for the patient's chest with your scalpel to cut back the flesh.
Step 4: Clamp bleeders with your hemostat.
Step 5: Retract skin with your retractor.
Step 6: Extract the implant with your hemostat.
Step 7: Close the wound with cautery.
Appendectomy
If it's useless, tear it out.
Step 1: Place the patient onto the operating table.
Step 1.5: Use a tank of anesthetic and a breath mask to make your patient sleep. (Optional)
Step 2: Place drapes over the patient's groin.
Step 3: Aim for the patient's groin, and cut the skin with your scalpel.
Step 4: Use your hemostat to clamp any bleeders.
Step 5: Use your retractor to open the incision.
Step 6: Use your scalpel to sever the appendix.
Step 7: 
Use your BARE HANDS to pull out the appendix.
Step 7.5: Dispose of the newly extracted appendix / eat the appendix / force feed it to the patient. (Optional)
Step 8: Cauterize the wound with the cautery.
Step 9: Wake up your patient and congratulate them on overcoming appendicitis!
Xenomorph Removal
GET IT OUT OF ME!!
Step 1: Place the patient onto the operating table.
Step 1.5: Use a tank of anesthetic and a breath mask to make your patient sleep. (Optional)
Step 2: Place drapes over the patient's chest.
Step 3: Use your scalpel to cut through the chest.
Step 4: Use your retractor to retract the skin.
Step 5: Use your saw to cut through the chest.
Step 6: Use your hemostat to pull out the larva.
Step 7: Close the wound with cautery.
Step 8: Congratulations! Your patient lives!
Lipoplasty
Why did I eat three whole pizzas?
Step 1: Place the patient onto the operating table.
Step 1.5: Use a tank of anesthetic and a breath mask to make your patient sleep. (Optional)
Step 2: Place drapes over the patient's chest.
Step 3: Use your scalpel to cut through the chest.
Step 4: Clamp bleeders with the hemostat.
Step 5: Slice up the fat with the saw.
Step 6: Remove the fat with the retractor
Step 7: Close the wound with cautery.
Step 8: Feed the patient his own fat as a lesson in vicious circles. (Optional)
Plastic Surgery
I need to disappear forever!
Step 1: Place the patient onto the operating table.
Step 1.5: Use a tank of anesthetic and a breath mask to make your patient sleep. (Optional)
Step 2: Place drapes over the patient's head to prepare for plastic surgery.
Step 3: Use your scalpel to make an incision in the head.
Step 4: Use your retractor to retract the skin around the incision.
Step 5: Use your scalpel to alter the patient's appearance.
Step 6: Use your cautery to mend the incision you made.
Step 7: Send that stranger to the HoP to finish his induction to the witness relocation program.
Gender Reassignment
For when something other than xeno scum is trapped in your body.
Step 1: Place the victim patient onto the operating table.
Step 1.5: Use a tank of anesthetic and a breath mask to make your patient sleep. (Optional)
Step 2: Place drapes over the patient's groin.
Step 3: Use your scalpel to cut through the groin.
Step 4: Clamp bleeders with the hemostat.
Step 5: Use the scalpel to carefully reshape the patient's... body.
***This actually applies their body-weight in estrogen or testosterone instantly, the scalpel acts as a giant syringe in this case.
Step 6: Close the wound with cautery.
Step 7: Perform plastic surgery to acquire a new gender appropriate name (Optional)
Cavity Implant
My god, he's a ticking timebomb!
Step 1: Place the patient onto the operating table.
Step 1.5: Use a tank of anesthetic and a breath mask to make your patient sleep. (Optional)
Step 2: Place drapes over the patient's chest.
Step 3: Use your scalpel to cut through the chest.
Step 4: Clamp bleeders with the hemostat.
Step 5: Use your retractor to pull back the skin.
Step 6: Use your scalpel to cut through to a cavity.
Step 7: Carefully place an item in the cavity / Use your hands to check for items in the cavity.
Step 8: Close the wound with cautery.
Augmentation
We can rebuild him... We have the technology.
Note: The head, torso, arms, and legs can all be augmented.
Step 1: Create the cyborg limb(s) using an exosuit fabricator.
Step 2: Place drapes over the limb you want to augment.
Step 3: Aim for the limb you want to replace with your scalpel to cut back the skin.
Step 4: Clamp bleeders with the hemostat.
Step 5: Use your retractor to pull back the skin.
Step 6: Use your scalpel to sever the muscles.
Step 7: Use your saw to cut through the limb.
Step 8: Use the cyborg limb on the limb you want to augment.
Ghetto Surgery
It is possible to perform surgery with improvised items, but the chance to complete each step will greatly decrease.
If you can't find an operating table, have no fear, you can fix someone up anywhere! Any table or bed will do, and even the floor if you have no other choice. It will reduce the chance of successfully completing a step, however.
Eye Surgery
Step 1: Place the patient onto any table.
Step 1.5: Knock the patient out for anesthetic. (Optional)
Step 2: Place a bedsheet over the patient's eyes.
Step 3: Aim for the patient's eyes, and cut the skin around them with a kitchen knife (65%) / shard (45%).
Step 4: Use a screwdriver (45%) / wirecutters (35%) to lift up the eyes.
Step 5: Use a wirecutters (60%) / cable coil (15%) to stop any potential bleeding.
Step 6: Use screwdriver (45%) / pen (25%) again to fix the patient's eyes.
Step 7: Use a welding tool (70%) / lighter (45%) / match (20%) to seal the wound.
Step 8: Wake up your patient, congratulate them on their new vision.
Brain Removal
Step 1: Place the patient onto any table.
Step 1.5: Knock the patient out for anesthetic. (Optional)
Step 2: Place a bedsheet over the patient's head.
Step 3: Aim for the patient's head with a kitchen knife (65%) / shard (45%) to cut back the flesh.
Step 4: Clamp bleeders with the wirecutters (60%) / cable coil (15%).
Step 5: Retract tissue with screwdriver (45%) / wirecutters (35%).
Step 6: Cut through the skull with a hatchet (35%) / butcher's cleaver (25%) / changeling's arm blade (75%).
Step 7: Extract the brain with the crowbar (55%).
Step 8: Deal with the brain, typically by putting it in an MMI and then giving it to a roboticist.
Step 9: Morgue the body.
Putting a brain back in:
Step 1: Place the patient onto any table.
Step 2: Cram their brain back into their skull.
Step 3: Usually, you take the body to be cloned.
Xenomorph Brain Surgery
Step 1: Place the patient onto any table.
Step 1.5: Use a tank of anesthetic and a breath mask to make your patient sleep. (Optional) Anesthetic cannot be used on Xenomorphs. Enjoy their screams of pain.
Step 2: Place a bedsheet over the patient's head.
Step 3: Cut through the skull with a hatchet (35%) / butcher's cleaver (25%) / changeling's arm blade (75%).
Step 4: Aim for the patient's head with a kitchen knife (65%) / shard (45%) to cut back the flesh.
Step 5: Retract tissue with screwdriver (45%) / wirecutters (35%).
Step 6: Cut through the skull with a hatchet (35%) / butcher's cleaver (25%) / changeling's arm blade (75%).
Step 7: Extract the brain with the crowbar (55%).
Step 8: Deal with the brain, typically by putting it in an MMI and then giving it to a roboticist. Alternatively, let genetics make a new person from the brain to fight the alien horde.
Step 9: Morgue the body. The chef might also like the body to make some tasty Xeno Burgers.
Implant Removal
Step 1: Place the patient onto any table.
Step 1.5: Knock the patient out for anesthetic. (Optional)
Step 2: Place a bedsheet over patient's chest.
Step 3: Aim for the patient's chest with a kitchen knife (65%) / shard (45%) to cut back the flesh.
Step 4: Clamp bleeders with a wirecutters (60%) / cable coil (15%).
Step 5: Retract skin with a screwdriver (45%) / wirecutters (35%).
Step 6: Extract the implant with a crowbar (65%).
Step 7: Close the wound with welding tool (70%) / lighter (45%) / match (20%).
Appendectomy
Step 1: Place the patient onto any table.
Step 1.5: Knock the patient out for anesthetic. (Optional)
Step 2: Place a bedsheet over the patient's groin.
Step 3: Aim for the patient's groin, and cut the skin with a kitchen knife (65%) / shard (45%).
Step 4: Use a wirecutters (60%) / cable coil (15%) to clamp any bleeders.
Step 5: Use a screwdriver (45%) / wirecutters (35%) to open the incision.
Step 6: Use a kitchen knife (65%) / shard (45%) to sever the appendix.
Step 7: Use your BARE HANDS to pull out the appendix.
Step 7.5: Dispose of the newly extracted appendix / eat the appendix / force feed it to the patient. (Optional)
Step 8: Cauterize the wound with the welding tool (70%) / lighter (45%) / match (20%).
Step 9: Wake up your patient and congratulate them on overcoming appendicitis!
Xenomorph Removal
Step 1: Place the patient onto any table.
Step 1.5: Knock the patient out for anesthetic. (Optional)
Step 2: Place a bedsheet over the patient's chest.
Step 3: Use a kitchen knife (65%) / shard (45%) to cut through the chest.
Step 4: Use a screwdriver (45%) / wirecutters (35%) to retract the skin.
Step 5: Use a hatchet (35%) / butcher's cleaver (25%) / changeling's arm blade (75%) to cut through the chest.
Step 6: Use a spade (65%) / minihoe (50%) / crowbar (35%) to pull out the larva.
Step 7: Close the wound with welding tool (70%) / lighter (45%) / match (20%).
Step 8: Congratulations! Your patient lives!
Lipoplasty
Step 1: Place the patient onto any table.
Step 1.5: Knock the patient out for anesthetic. (Optional)
Step 2: Place a bedsheet over the patient's chest.
Step 3: Use a kitchen knife (65%) / shard (45%) to cut through the chest.
Step 4: Clamp bleeders with the wirecutters (60%) / cable coil (15%).
Step 5: Slice up the fat with the hatchet (35%) / butcher's cleaver (25%).
Step 6: Remove the fat with the screwdriver (45%) / wirecutters (35%)
Step 7: Close the wound with welding tool (70%) / lighter (45%) / match (20%).
Step 8: Feed the patient his own fat as a lesson in vicious circles. (Optional)
Plastic Surgery
Step 1: Place the patient onto any table.
Step 1.5: Knock the patient out for anesthetic. (Optional)
Step 2: Place a bedsheet over the patient's head to prepare for plastic surgery.
Step 3: Use a kitchen knife (65%) / shard (45%) to make an incision in the head.
Step 4: Use a screwdriver (45%) / wirecutters (35%) to retract the skin around the incision.
Step 5: Use a kitchen knife (50%) / wirecutters (35%) to alter the patient's appearance.
Step 6: Use a welding tool (70%) / lighter (45%) / match (20%) to mend the incision you made.
Step 7: Send that stranger to the HoP to finish his induction to the witness relocation program.
Gender Reassignment
Step 1: Place the victim patient onto any table.
Step 1.5: Knock the patient out for anesthetic. (Optional)
Step 2: Place a bedsheet over the patient's groin.
Step 3: Use a kitchen knife (65%) / shard (45%) to cut through the groin.
Step 4: Clamp bleeders with the wirecutters (60%) / cable coil (15%).
Step 5: Use the hatchet (oh my God) (50%) / wirecutters (35%) to carefully reshape the patient's... body.
Step 6: Close the wound with welding tool (70%) / lighter (45%) / match (20%).
Step 7: Perform plastic surgery to acquire a new gender appropriate name (Optional)
Cavity Implant
Step 1: Place the patient onto any table.
Step 1.5: Knock the patient out for anesthetic. (Optional)
Step 2: Place a bedsheet over the patient's chest.
Step 3: Use a kitchen knife (65%) / shard (45%) to cut through the chest.
Step 4: Clamp bleeders with the wirecutters (60%) / cable coil (15%).
Step 5: Use a screwdriver (45%) / wirecutters (35%) to pull back the skin.
Step 6: Use a kitchen knife (65%) / shard (45%) to cut through to a cavity.
Step 7: Carefully place an item in the cavity / Use your hands to check for items in the cavity.
Step 8: Close the wound with welding tool (70%) / lighter (45%) / match (20%).
Augmentation
Note: The head, torso, arms, and legs can all be augmented.
Step 1: Create the cyborg limb(s) using an exosuit fabricator.
Step 2: Place a bedsheet over the limb you want to augment.
Step 3: Aim for the limb you want to replace with a kitchen knife (65%) / shard (45%) to cut back the skin.
Step 4: Clamp bleeders with the wirecutters (60%) / cable coil (15%).
Step 5: Use a screwdriver (45%) / wirecutters (35%) to pull back the skin.
Step 6: Use a kitchen knife (65%) / shard (45%) to sever the muscles.
Step 7: Use a hatchet (35%) / butcher's cleaver (25%) / changeling's arm blade (75%) to cut through the limb.
Step 8: Use the cyborg limb on the limb you want to augment.