A medical device apparatus comprising: a first entry guide comprising a first channel configuration, the first channel configuration of the first entry guide comprising a first instrument channel; a second entry guide comprising a second channel configuration different from the first channel configuration of the first entry guide, the second channel configuration of the second entry guide comprising a first instrument channel; and a surgical system comprising an entry guide manipulator, one of the first entry guide and the second entry guide being mounted in the entry guide manipulator, the entry guide manipulator comprising an entry guide manipulator assembly, a lateral motion mechanism, and an instrument manipulator (240C1) coupled to the lateral motion mechanism, the entry guide manipulator assembly being configured to rotate the lateral motion mechanism and the instrument manipulator around a roll axis of the entry guide manipulator assembly; wherein with the entry guide manipulator assembly remaining stationary about the roll axis, the lateral motion mechanism is configured to move the instrument manipulator (240C1) to a first predetermined location on a condition that the first entry guide is mounted in the entry guide manipulator, so that a shaft (262C1) of an instrument (260C1) coupled to the instrument manipulator (240C1) is aligned with the first instrument channel of the first entry guide; and wherein with the entry guide manipulator assembly remaining stationary about the roll axis, the lateral motion mechanism is configured to move the instrument manipulator (240C1) to a second predetermined location, different from the first predetermined location, on the condition that the second entry guide is mounted in the entry guide manipulator, so that a shaft (262C1) of an instrument (260C1) coupled to the instrument manipulator (240C1) is aligned with the first instrument channel of the second entry guide. a first entry guide comprising a first channel configuration, the first channel configuration of the first entry guide comprising a first instrument channel; a second entry guide comprising a second channel configuration different from the first channel configuration of the first entry guide, the second channel configuration of the second entry guide comprising a first instrument channel; and a surgical system comprising an entry guide manipulator, one of the first entry guide and the second entry guide being mounted in the entry guide manipulator, the entry guide manipulator comprising an entry guide manipulator assembly, a lateral motion mechanism, and an instrument manipulator (240C1) coupled to the lateral motion mechanism, the entry guide manipulator assembly being configured to rotate the lateral motion mechanism and the instrument manipulator around a roll axis of the entry guide manipulator assembly; wherein with the entry guide manipulator assembly remaining stationary about the roll axis, the lateral motion mechanism is configured to move the instrument manipulator (240C1) to a first predetermined location on a condition that the first entry guide is mounted in the entry guide manipulator, so that a shaft (262C1) of an instrument (260C1) coupled to the instrument manipulator (240C1) is aligned with the first instrument channel of the first entry guide; and wherein with the entry guide manipulator assembly remaining stationary about the roll axis, the lateral motion mechanism is configured to move the instrument manipulator (240C1) to a second predetermined location, different from the first predetermined location, on the condition that the second entry guide is mounted in the entry guide manipulator, so that a shaft (262C1) of an instrument (260C1) coupled to the instrument manipulator (240C1) is aligned with the first instrument channel of the second entry guide.