In Microsurgeon, the player is a surgeon who controls a microscopic robot probe throughout a patient's body attempting to treat various illness and diseases before those ailments terminate the patient. The diseases the patient can suffer from including bacterial infections, brain tumors, cholesterol blockages in arteries, tapeworms, and various diseases of specific organs.

The player gets a quick chance to review the patient's chart before the game begins, giving him/her the opportunity to evaluate where he/she needs to focus attention on the patient the quickest. It's generally most effective to treat the areas that are the most critical initially, and then focus on other areas as the progress or as other conditions are cured.

The robot probe has three different treatment regimens that can be used including ultrasonic rays, antibiotics, and aspirin. The ultrasonic rays treat most conditions found during the game. Antibiotics are used to treat the various bacterial infections that appear in a patient. Aspirin can temporarily disable a virus.