Classical molecular dynamics simulations are used to examine the indentation of monolayers composed of linear hydrocarbon chains with 8, 13, or 22 carbon atoms that are chemically bound (or anchored) to a diamond (111) substrate. Indentation is accomplished using both a flexible and rigid single-wall, capped [10,10] nanotube as the tip. Regardless of the nanotube used, the simulations show that indentation of the hydrocarbon monolayers causes a disruption of the original ordering of the monolayer, pinning of selected hydrocarbon chains beneath the tube, and the formation of gauche defects within the monolayer. Because nanotubes are stiff along their axial direction, the flexible nanotube is distorted only slightly by its interaction with the softer monolayers. However, interaction with the hard diamond substrate causes the tube to buckle. Severe indents with a rigid nanotube tip result in rupture of chemical bonds within the hydrocarbon monolayer.