A method for forming a standoff structure for packaging devices, e.g., optical devices, integrated circuit devices. The method includes providing a substrate, e.g., silicon wafer. The substrate includes a first surface region, a second surface region, and a thickness defined between the first surface region and the second surface region. The method includes protecting selected portions of the first surface region using a masking layer while leaving a plurality of unprotected regions. Preferably, each of the unprotected regions is to be associated with an opening through the thickness of the substrate. The method causes removal of the plurality of unprotected regions to form a plurality of openings through the thickness of the substrate to provide a resulting patterned substrate. Each of the openings is bordered by a portion of the selected portions of the first surface region. Preferably, etching techniques, such as wet etch or dry etching, can be used, depending upon the embodiment. The method removes the masking layer via ashing or stripping. In a specific embodiment, the method further includes bonding a handle substrate to the patterned substrate. Preferably, the handle substrate is optically transparent. Each of the openings is bordered by a portion of the handle substrate to form a recessed region.