High rake angle orthogonal machining of highly ordered pyrolytic graphite (HOPG) parallel to the basal plane was carried out to synthesize few layers of graphene. The quality of the graphite sheets was found to be an alliance of any pre-existing defects in the HOPG and the nature of the machining process itself. Presence of pre-existing defects such as kinks and discontinuous layers were observed during the lateral examination of HOPG structure prior to machining. Evidence of flat, folded, and rolled structures were found in exfoliated graphite sheets in addition to defects such as two types of kink bands. Multiple spikes in measured cutting forces were seen during machining due to disturbances in tool movement. Molecular dynamic simulations were carried out to support the argument that specific pre-existing defects such as discontinuous layers cause the marked disturbances during machining.