A system configured to transform a control frame of a medical instrument configured to be inserted into a patient, the system comprising: at least one computer-readable memory having stored thereon executable instructions; and one or more processors in communication with the at least one computer-readable memory and configured to execute the instructions to cause the system to at least: identify a control frame of reference representing a relationship between a motor control command and a motor output of the medical instrument, the medical instrument including an imaging device positioned at a distal end of the medical instrument; determine a tip frame of reference based on one or more features derived from at least one image of an anatomical feature, wherein the at least one image of the anatomical feature is based on data from the imaging device (315, 356, or 456), the tip frame of reference representing a current orientation of the distal end of the medical instrument; obtain a desired frame of reference representing a frame of reference relative to an anatomy frame of reference, wherein the desired frame of reference is based on one or more features derived from at least one model of the anatomical feature; detect a difference between the tip frame of reference and the desired frame of reference based on comparing the one or more features derived from the at least one image of the anatomical feature and the one or more features derived from the at least one model of the anatomical feature; determine an adjustment to the control frame of reference based on the difference between the tip frame of reference and the desired frame of reference; and transform the control frame of reference by rotating the control frame of reference based on the determined adjustment such that the control frame of reference is aligned with the desired frame of reference. at least one computer-readable memory having stored thereon executable instructions; and one or more processors in communication with the at least one computer-readable memory and configured to execute the instructions to cause the system to at least: identify a control frame of reference representing a relationship between a motor control command and a motor output of the medical instrument, the medical instrument including an imaging device positioned at a distal end of the medical instrument; determine a tip frame of reference based on one or more features derived from at least one image of an anatomical feature, wherein the at least one image of the anatomical feature is based on data from the imaging device (315, 356, or 456), the tip frame of reference representing a current orientation of the distal end of the medical instrument; obtain a desired frame of reference representing a frame of reference relative to an anatomy frame of reference, wherein the desired frame of reference is based on one or more features derived from at least one model of the anatomical feature; detect a difference between the tip frame of reference and the desired frame of reference based on comparing the one or more features derived from the at least one image of the anatomical feature and the one or more features derived from the at least one model of the anatomical feature; determine an adjustment to the control frame of reference based on the difference between the tip frame of reference and the desired frame of reference; and transform the control frame of reference by rotating the control frame of reference based on the determined adjustment such that the control frame of reference is aligned with the desired frame of reference. identify a control frame of reference representing a relationship between a motor control command and a motor output of the medical instrument, the medical instrument including an imaging device positioned at a distal end of the medical instrument; determine a tip frame of reference based on one or more features derived from at least one image of an anatomical feature, wherein the at least one image of the anatomical feature is based on data from the imaging device (315, 356, or 456), the tip frame of reference representing a current orientation of the distal end of the medical instrument; obtain a desired frame of reference representing a frame of reference relative to an anatomy frame of reference, wherein the desired frame of reference is based on one or more features derived from at least one model of the anatomical feature; detect a difference between the tip frame of reference and the desired frame of reference based on comparing the one or more features derived from the at least one image of the anatomical feature and the one or more features derived from the at least one model of the anatomical feature; determine an adjustment to the control frame of reference based on the difference between the tip frame of reference and the desired frame of reference; and transform the control frame of reference by rotating the control frame of reference based on the determined adjustment such that the control frame of reference is aligned with the desired frame of reference.