A medical instrument system includes a control system and an operator input device coupled to an instrument including a sensor. The control system includes a processor and memory comprising instructions that cause the control system to: determine a distance between a distal tip of the instrument and an anatomical area based on sensor data; determine a motion scaling parameter based on the distance; receive an input instruction from the operator input device; map the input instruction to an output instruction including applying the motion scaling parameter to the input instruction to create the output instruction; instruct an actuator to move the instrument based on the output instruction; determine a second distance between the distal tip and the anatomical area based on the sensor data; determine a second motion scaling parameter based on the second distance; and stop movement of the instrument based on the second motion scaling parameter.