We present the development of a fabrication technique for a semiconductor-based photonic crystal (PhC) nano-membrane device with reconfigurable active waveguides using micro-electro-mechanical systems (MEMS) technology. This device can be used as a basic building block for optoelectronic integrated circuits that can be reprogrammed for different functionalities such as switches, modulators, time delay lines, resonators, etc. The device is fabricated three-dimensionally on GaAs/Alx1GaAs/Alx2GaAs epitaxial layers on a GaAs substrate. The device has a top PhC membrane layer structure composed of hexagonal holes in a triangular lattice. Below that, a separate suspended bridge layer can insert a line of posts into the PhC holes to create a defect line. This MEMS feature can generate/cancel a section of the waveguide in the PhC platform, or (by partial removal) it can change the dispersion of the waveguide. Therefore, the same structure can be used as different types of devices. In this paper, we will discuss detailed fabrication processes for such a multi-layer 3D device structure, including e-beam lithography, inductively coupled plasma reactive ion etching, and multiple steps of regular photolithography and selective wet chemical etching. The unique processing sequence allows us to fabricate the multi-layer 3D device structure from one top surface without regrowth, wafer bonding, or access from the back surface. This simplifies the device processing and reduces the fabrication cost.