Flexible endoscopes are used in many surgical procedures and diagnostic exams. They have also been used recently for new surgical procedures using natural orifices called NOTES. While these procedures are really promising for the patients, they are really awkward for the surgeons. In order to assist the surgeon, physiological motion cancellation has been successfully applied on a robotized endoscope in L. Ott, et al., (May 19-23, 2008), by using a prototype repetitive controller (PRC) and a repetitive generalized predictive controller (R-GPC). Both controllers showed to be powerful tools to cancel periodic disturbances but with poor transient response to non-periodic disturbances. Contrary to the R-GPC, the PRC is unsuitable for handling non-periodic reference changes. We propose in this paper, as a first improvement, a model-based control scheme using the PRC which allows to decouple the reference tracking from the periodic output disturbance rejection. The response to nonperiodic disturbance is also improved by this technique but a repetition appears caused by the repetitive controller. As a second improvement, a switching control scheme is proposed to avoid the repetition.