  Transition metal dichalcogenides (TMDCs) have attracted significant attention
for optoelectronic, photovoltaic and photoelectrochemical applications. The
properties of TMDCs are highly dependent on the number of stacked atomic
layers, which is usually counted post-fabrication, using a combination of
optical methods and atomic force microscopy (AFM) height measurements. Here, we
use photoluminescence spectroscopy and three different AFM methods to
demonstrate significant discrepancies in height measurements of exfoliated
MoSe$_2$ flakes on SiO$_2$ depending on the method used. We highlight that
overlooking effects from electrostatic forces, contaminants and surface binding
can be misleading when measuring the height of a MoSe$_2$ flake. These factors
must be taken into account as a part of the protocol for counting TMDC layers.
