Physical and photolithographic techniques are commonly used to create chemical patterns for a range of technologies including cell Culture Studies, bioarrays and other biomedical applications. In this paper, we describe the Fabrication of chemical micropatterns from commonly used plasma polymers, Atomic force microcopy (AFM) imaging, time-of-flight static secondary ion mass spectrometry (ToF-SSIMS) imaging, and multivariate analysis have been employed to visualize the clinical boundaries created by these patterning techniques and assess the spatial and chemical resolution of the patterns. ToF-SSIMS analysis demonstrated that well-defined chemical and spatial boundaries were obtained from photolithographic patterning, while the resolution of physical patterning via a transmission electron microscopy (TEM) grid varied depending on the properties of the plasma system including the substrate material. In general, physical masking allowed diffusion of the plasma species below the mask and bleeding of the surface chemistries. Multivariate analysis techniques including principal component analysis (PCA) and region of interest (ROI) assessment were used to investigate the ToF-SSIMS images of a range of different plasma polymer patterns. In the most challenging case, where two strongly reacting polymers, allylamine and acrylic acid were deposited, PCA confirmed the fabrication of micropatterns with defined spatial resolution. ROI analysis allowed for the identification of an interface between the two plasma polymers for patterns fabricated using the photolithographic technique which has been previously overlooked. This study clearly demonstrated the versatility of photolithographic patterning for the production of multichemistry plasma polymer arrays and highlighted the need for complementary characterization and analytical techniques during the Fabrication plasma polymer micropatterns,