A method and apparatus are disclosed for forming an optical trap with light directed through or above a semiconductor material. A preferred embodiment selected light-trapping wavelengths that have lower absorption by the semiconductor. A preferred embodiment provides for an optical trapping through semiconductor employing a thin silicon (Si) wafer as a substrate. Further embodiments of the invention provide for microchannel fabrication, force probe measurement, sorting, switching and other active manipulation and assembly using an optical trap.