To perform a tool exchange in a medical robotic system, tool is retracted back into an entry guide from a deployed position and pose so that an assistant in the operating room may replace it with a different tool. While the tool is being retracted back towards the entry guide by user action, its configuration is changed to an entry pose while avoiding collisions with other objects so that it may fit in the entry guide. After the tool exchange is completed, a new tool is inserted in the entry guide and extended out of the guide by user action to the original position of the old tool prior to its retraction into the entry guide while the tool's controller assists the user by reconfiguring the new tool so as to resemble the original deployed pose of the old tool prior to its retraction into the entry guide.