A system and method to compensate for respiratory motion in imaging of instruments introduced into the subject anatomy is provided. The system can include an imaging system in communication with a controller. The controller can include a memory with program instructions for execution by the processor to perform the steps of: detecting an illustration of at least a portion of the plurality of instruments introduced into the subject anatomy in a first image and a second image, comparing and calculating a displacement of the plurality of instruments between the first and second images, calculating one of an average or median displacement of the plurality of instruments between the first and second images, and applying one of the average and the median displacement to adjust at least a portion of the first or second images or a pre-acquired three-dimensional model of the internal region of interest.