Surface morphology of thin molecular layer of 2,3-Iron-naphthalocyanine (2,3 FeNPc) was studied by scanning tunneling microscopy (STM) at the ambient conditions. Organic layer with thickness of 40 nm was vapour phase deposited on amorphous carbon substrate. The STM images have revealed the pecularities of surface molecular organization from large range (hundreds of nm) down to atomic scale. Arrays of locally ordered linear stuctures have been distinguished as the main morphological features of the examined surface. At several places the well-ordered STM patterns have been distinguished at the atomic scale. They can be described as stacks of periodicity approximatelly 0.4 nm in a row and 1.5 nm between stacks. These results can be explained by arrangement of 2,3-FeNPh molecules in stacks with a main plane being perpendicular to the substrate surface.