We report a simple method for identifying foldable viral surface protein fragments in a random but systematic manner. The method involves digestion and reassembly of a target gene to generate a pool of smaller DNA fragments with random ends but controllable lengths, followed by screening for foldable fragments using green fluorescent protein (GFP) as a folding reporter. The surface glycoproteins of SARS-CoV and HIV-1 were used as model proteins. Two foldable fragments for SARS-CoV spike protein were identified, which coincide with various anti-SARS-CoV peptides. A similar treatment of the HIV-1 gp120 yielded a number of fragments that are associated with the critical CD4 binding site, or the partially buried CCR5 binding site of the protein. The random dissection approach described here should be applicable to other viral proteins for isolating soluble viral surface protein fragments, and may provide alternatives to the full-length proteins (subunits) or linear short peptides in search for antigen or vaccine candidates.