A surgical system uses a single entry port in a wide variety of surgeries. To insert multiple surgical instruments into a patient through a single entry port requires that the shaft of at least one of the surgical instruments be bent between the base of the surgical instrument and the point where the shaft contacts a channel in an entry guide. Each surgical instrument is positioned by an instrument manipulator positioning system so that when the shaft is inserted in a channel of the entry guide, any bending of the shaft does not damage the surgical instrument and does not inhibit proper operation of the surgical instrument.