Systems and methods for monitoring an operative site during a surgical procedure using a computer controlled surgical device. In general the methods include the steps of processing one or more defined cutting paths having one or more cut regions; determining a correlation between the cut region and one or more critical regions to generate an alert, wherein the alert indicates a movable end-effector is within a defined proximity of the critical region; and requiring a user acknowledgment of the alert to allow processing of the cutting path to continue. Also described herein are systems and methods for minimizing user fatigue during a semi-computer controlled surgical procedure. In general the methods includes the step of requiring a user generated acknowledgment in response to a computer generated alert, wherein the user acknowledgment is generated using a user controller, the user controller being minimally intrusive to the user experience.
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