A multichamber single‐wafer chemical vapor deposition reactor has been designed and built for ultrahigh vacuum, low temperature, selective silicon epitaxy. The reactor is equipped withinsitumonitors for study and control of both predeposition wafer cleaning and epitaxial growth process. A detailed description of the system and its preliminary performance are reported. An argon or helium plasma excited by electron cyclotron resonance (ECR) has been used for predeposition wafer cleaning. Results of the ECR plasma characterization by a Langmuir probe are presented. Furthermore, structural quality of the wafers subjected to plasma cleaning were evaluated by Rutherford backscattering spectroscopy and scanning electron microscopy. Results showed that a damage free substrate can potentially be achieved at a wafer temperature of 500 °C.