We discuss a process for selective area deposition of microcrystalline silicon (μc-Si) using plasma enhanced chemical vapor deposition at low substrate temperature (<300°C) using time modulated silane flow in a hydrogen plasma. We discuss selectivity and deposition rate on a variety of substrates with process conditions important for manufacturing applications, and show a distinct microstructural evolution in the initial nucleation layers using Raman spectroscopy that correlates with the transition from selective to non-selective growth. Atomic hydrogen discriminates between different degrees of bond strain in the nucleii formed on different substrates, and can increase the crystallinity fraction in films deposited at low temperatures by modifying the kinetics of bulk-like bond formation.