In a method for imaging a solid state substrate, a vapor is condensed to an amorphous solid water condensate layer on a surface of a solid state substrate. Then an image of at least a portion of the substrate surface is produced by scanning an electron beam along the substrate surface through the water condensate layer. The water condensate layer integrity is maintained during electron beam scanning to prevent electron-beam contamination from reaching the substrate during electron beam scanning. Then one or more regions of the layer can be locally removed by directing an electron beam at the regions. A material layer can be deposited on top of the water condensate layer and any substrate surface exposed at the one or more regions, and the water condensate layer and regions of the material layer on top of the layer can be removed, leaving a patterned material layer on the substrate.