Monolayer assemblies on silicon and silica surfaces are of interest for a number of technological reasons, such as substrates in micro-arrays, surface passivation in MEMS, and monolayer mask in soft-lithography. I present novel approaches for the formation of molecular monolayers on silicon and silica surfaces. These approaches rely on a two-step strategy: in the first step, a silicon or silica surface is activated to give reactive functional groups; in the second step, the activated surface reacts with simple organic molecules for monolayer assembly. Examples of alkyl, aromatic, and PEG monolayer assemblies will be presented and their applications in MEMS and micro-arrays will be demonstrated.