This paper presents a Visually Guided Micro Positioning and Alignment System that employs Scanning White Light Interferometry (SWLI). An Interferometry microscope is integrated with a magnetically suspended motion stage to achieve alignment of micro objects in 3D. Based on the SWLI measurement an integrated control scheme is presented which enables the alignment of micro objects in 3D space. A demonstration of 3D micro alignment and manipulation was designed to show the capabilities of the integrated system. Alignment and docking of two silicon micro cantilevers is demonstrated using the magnetically suspended stage and the 3D sensing ability of the SWLI. Experimental results show that cantilever docking can be achieved with less than 30nN force sensitivity.