Precision nanoscale deposition is a fundamental requirement for much of current nanoscience research and promises to facilitate exciting industrial applications. Tailoring chemical composition and surface structure on the sub-100 nm scale benefits researchers in topics ranging from catalysis, to biological recognition in nanoscale systems, to electronic connectivity on the nanoscale. Precision nanoscale deposition engenders applications such as additive photomask repair and nanodevice fabrication. Dip Pen Nanolithography (DPN) is a scanning-probe-based direct-write technique for generating surface-patterned chemical functionality and discrete structures on the sub-100 nm scale. In this publication we explore the effects of changing tip radius and surface roughness. We find that blunter tips lead to higher minimum line widths and that higher rms surface roughness leads to higher minimum line widths; line edge roughness also increases with substrate roughness and surface feature size. Also, we characterize the performance of the Nscriptor DPN instrument and demonstrate the placement of pattern features with precision better than 10 nm, and size control better than 15% for sub-100 nm features.