We have obtained nanometer-scale scanning tunneling microscope images of individual, randomly-spaced immunoglobulin G (IgG) and chaperonin molecules in ultrahigh vacuum. The methodology developed for routine imaging includes the use of a sputter-deposited Au(lll) substrate for deposition, tunneling tip with diameters smaller than 10 nm, very dilute concentration of protein molecules in a volatile buffer for molecular deposition, and a vacuum environment for preserving the molecules for imaging for about 2 weeks. The imaged structures of both molecules agree well with X-ray data. Compression of the vertical dimension of the molecule was severe only in the relatively thick (14.6 nm) chaperonin but not in the thin (similar to 4 nm) IgG. Effects such as degradation and cleavage of individual molecules were also observed. An evaluation of the existing proposed imaging mechanisms is presented.