Abstract: According to one aspect of the invention a plasma-based substrate processing apparatus comprises a collimator holding device, which efficiently and accurately positions a collimator over a substrate to enable the plasma-based substrate processing apparatus to selectively deposit and/or remove material at the bottom of a high aspect ratio openings or trenches and/or protrusions. The collimator holding device may comprise a holder ring, with adjustable spacers, having the means of manually positioning a collimator a precise distance above and approximately parallel to the wafer support, while providing greater heat capacity and heat transfer rates, thus reducing the risk of thermal damage to the collimator. In an embodiment, the holder ring may further comprise one or more slots, which may provide ventilation for a mini-chamber above the substrate being processed.