A modular manipulation system and method for using such modular manipulation system for manipulating a sample under study with a microscope are provided. According to at least one embodiment, a platform is provided that comprises an interface to a microscope, a sample stage, and a plurality of interfaces for receiving manipulator modules for manipulating a sample arranged on the sample stage. Preferably, the plurality of interfaces for receiving manipulator modules are each capable of detachably coupling a manipulator module to the platform. Thus, in a preferred embodiment, a user may selectively couple one or more desired manipulator modules to the platform to enable a desired type of manipulation to be performed on a sample under study. Accordingly, a preferred embodiment enables great flexibility in configuring a manipulation system in a desired manner.