One embodiment of the present invention provides a process for obtaining high-quality boundaries for individual multilayer structures which are fabricated on a trench-partitioned substrate. During operation, the process receives a trench-partitioned substrate wherein the substrate surface is partitioned into arrays of isolated deposition platforms which are separated by arrays of trenches. The process then forms a multilayer structure, which comprises a first doped layer, an active layer, and a second doped layer, on one of the deposition platforms. Next, the process removes sidewalls of the multilayer structure.