A method of controlling an elongate instrument during a medical procedure involving motion of the elongate instrument relative to a patient is provided. The method includes generating, by a control system, a first model of the elongate instrument, and generating, by the control system, a second model of the elongate instrument based on a reference pose of the elongate instrument. The method further includes comparing, by the control system, the first model with the second model and determining, by the control system, a state of a system configuration based on the comparison.
