We demonstrate the integration of micro-electro-mechanical-systems (MEMS) scanning mirrors as active elements for the local optical pumping of ultra-cold atoms in a magneto-optical trap. A pair of MEMS mirrors steer a focused resonant beam through a cloud of trapped atoms shelved in the F = 1 ground-state of 87 Rb for spatially selective fluorescence of the atom cloud. Two-dimensional control is demonstrated by forming geometrical patterns along the imaging axis of the cold atom ensemble. Such control of the atomic ensemble with a microfabricated mirror pair could find applications in single atom selection, local optical pumping, and arbitrary cloud shaping. This approach has significant potential for miniaturization and in creating portable control systems for quantum optic experiments.