Functional integration of optical trapping techniques with silicon surfaces and environments can be realized with minimal modification of conventional optical trapping instruments offering a method to manipulate, track and position cells or non-biological particles over silicon substrates. This technique supports control and measurement advances including the optical control of silicon-based microfluidic devices and precision single molecule measurement of biological interactions at the semiconductor interface. Using a trapping laser in the near infra-red and a reflective imaging arrangement enables object control and measurement capabilities comparable to trapping through a classical glass substrate. The transmission efficiency of the silicon substrate affords the only reduction in trap stiffness. We implement conventional trap calibration, positioning, and object tracking over silicon surfaces. We demonstrate control of multiple objects including cells and complex non-spherical objects on silicon wafers and fabricated surfaces.