Two-dimensional PbSe nanocrystal arrays on silicon nitride membranes were investigated using electrostatic force microscopy (EFM) and transmission electron microscopy (TEM). Changes in lattice and transport properties upon annealing in a vacuum were revealed. Local charge transport behavior was directly imaged by EFM and correlated to nanopatterns observed with TEM. Charge transport through nanochannels in complex two-dimensional nanocrystal networks was identified. Our results demonstrate the importance of measurements of local transport details complementary to the conventional current-voltage (I-V) measurements.