Methods and apparatus for controlling microloading, such as within cell microloading between adjacent cells or isolated / dense microloading between areas of isolated or dense features during shallow trench isolation (STI) fabrication processes, or other trench fabrication processes, are provided herein. In some embodiments, a method for fabricating STI structures may include providing a substrate having a patterned mask layer formed thereon corresponding to one or more STI structures to be etched; etching the substrate through the patterned mask layer using a plasma formed from a process gas to form one or more STI structure recesses on the substrate; and pulsing the plasma for at least a portion of etching the substrate to control at least one of a depth or width of the one or more STI structure recesses.