Wrinkling of colloidal particles alter a wide variety of interfacial properties but quantitative topographical descriptions have been explored experimentally to a very limited extent. In this study, we present a harmonic analysis of surface wrinkles and folds on submicron colloidal particles, obtained using an aerosol flow route, with small radius (<300 nm) and high crust thickness-to-radius ratio (>0.1). The particle surface coordinates were mapped in their entirety using cryo-electron tomography and subsequently reconstructed using spherical harmonics, allowing a spectral topographical description of the instability patterns and the identification of their surface modes by lateral wavelength. Wrinkled and crumpled particles showed a similar surface roughness spectrum, wherein differences were found most noticeable in the large wavelength region. The analysis of preferred directions of harmonic frequencies indicated a possible axial or planar alignment attributed to the directionality of the surface corrugations. The employed characterization methodology can further the study of topographical influences on colloidal interactions.