Inorganic synthesis and materials chemistry have made it possible to synthesize and tailor the properties of nanoparticles for diverse applications. Nanoparticles have been conjugated with DNA, peptides, and antibodies to generate nanoparticle bioconjugates with hybrid functionalities that are useful for a broad range of applications in bioanalytical assays, targeted drug delivery and nanotechnology. Concurrent with development of synthetic approaches for nanoparticles, new measurements have evolved using scanning probe microscopy (SPM), providing unprecedented resolution and measurement capabilities for characterizations of the morphology and certain properties of nanoparticles and nanocrystals. New measurement technologies with SPM are still being invented, and the tools of SPM have been widely implemented by researchers in both academia and industry. The incentive and primary advantage for SPM measurements are the capabilities of reaching atomic and molecular resolution. Local surface modification can also be accomplished with SPM‐based lithographies. In this article, recent applications of SPM for nanoscale measurements and nanofabrication with different systems of nanoparticles and nanocrystals are reviewed. Scanning probe measurements provide unprecedented resolution for characterizing nanomaterials to investigate physical, chemical, and biochemical properties at the nanoscale. The advantages and limitations of SPM are also discussed, with descriptions of the various imaging and lithography modes that have been applied for characterizing nanoparticles.