Methods for making nanocodes that can be detected using scanning probe microscopy are provided, as are nanocodes constructed of two or more polymers, including homogeneous polymers such as nucleic acid molecules and heterogeneous polymers such as peptide nucleic acid polymers, and subunits useful for constructing such nanocodes. Also provided are modified nanocodes such as a nanocode containing one or more linked metals such as gold or iron and/or a linked probe that can specifically bind a target molecule. In addition, systems are provided that include such nanocodes, for example, a system that includes the nanocode and a surface and/or a scanning probe microscope probe. Methods of using such nanocodes, for example, to detect and/or identify a target molecule in a sample (e.g., a biological or environmental sample) using scanning probe microscopy, also are provided.