Investigations on lithographically formed cavities of surface-imprinted polymers (SIP) can help to gain deeper understanding on cell recognition with SIPs: it is known that surface topography and biomolecules transferred during surface imprinting contribute to cell adhesion. In this work, SIPs synthesized via two different imprinting techniques, namely stamp imprinting and polymerization of Pickering emulsions, were investigated and compared to each other, using atomic force microscopy (AFM) and Peak Force Quantitative Nano Mechanics (PF-QNM). We focused on SIPs based on poly(styrene-co-divinylbenzene) as model polymer and E. coli as model template for cell imprinting. Both imprinting approaches led to cavities that revealed nanostructures within the imprints. Stamp imprinting cavities feature low surface roughness and channel structures that resemble the negative pattern of the bacteria on the stamp and their filaments, while SIPs synthesized via polymerization of Pickering emulsions reveal globular nanostructures accumulating in the imprints. AFM phase imaging and adhesion mapping using PF-QNM show that these globular structures are remainders of the imprinted E. coli cells, most likely lipopolysaccarides, which is not observable in imprints resulting from stamp imprinting.