Atomic force microscopy (AFM) is a powerful tool that enables imaging and nanomechanical properties characterization of biological materials. Nanofibers are the structural units of many biological systems and their role in the development of advanced biomaterials is crucial. AFM methods have proven to be effective towards the characterization of fibers with respect to biological and bioengineering applications at the nanoscale. However, both the topographical and mechanical properties’ nanocharacterizations of single fibers using AFM are challenging procedures. In particular, regarding imaging procedures, significant artifacts may arise from tip convolution effects. The geometrical characteristics of the AFM tip and the nanofibers, and the fact that they have similar magnitudes, may lead to significant errors regarding the topographical imaging. In addition, the determination of the mechanical properties of nanofibers is also challenging due to their small dimensions and heterogeneity (i.e., the elastic half-space assumption is not valid in most cases). This review elucidates the origins of errors in characterizing individual nanofibers, while also providing strategies to address limitations in experimental procedures and data processing.