Using fibrinogen (Fg) protein as a probe molecule, mapping using accumulated probe trajectories (MAPT) is performed on nanostructured melt‐drawn high‐density poly(ethylene) (HDPE) films composed of well‐oriented crystalline patches separated by amorphous regions. The spatially grouped molecular trajectories allow for identification of regions with distinct surface properties (i.e., crystalline vs. amorphous) while simultaneously determining the characteristic dynamic protein behavior within those regions. In the presence of solution with a sufficiently high Fg concentration, discrete patches of a dense, ordered protein layer form (presumably on crystalline HDPE regions), leading to a dramatic rise in the surface residence time (by more than two orders of magnitude) of molecules incorporated into the film. Within this ordered Fg layer, individual molecules exhibit slow anisotropic lateral diffusion; the mobility is restricted by the nanostructure boundaries of the underlying HDPE. On HDPE films at low Fg surface coverage, or on films that have been rendered hydrophilic with Ar plasma, short surface residence times and fast, isotropic diffusion are observed. These results demonstrate the ability of spatially resolved single‐molecule tracking to provide mechanistic information about biomolecule‐surface interactions in a highly heterogeneous environment.