Paper-based platforms for biological studies have received significant attention given that cellulose is ubiquitous, biocompatible, and can be readily organized into tunable fibrous structures. In the latter form, effect of complexity in surface morphologies (roughness, porosity and fiber organization) on cell-substrate interaction has not been thoroughly explored. We infer that altering the properties of a fibrous material should lead to significant changes in cellular microenvironment and direct the deposition of structurally analogous extracellular matrix (fiber-fiber templating) like collagen. Here, we elucidate the effect of varying paper roughness and surface chemistry on NIH/3T3 fibroblasts via organization of excreted collagen. Collagen intensity was found to increase linearly with paper porosity, indicating a 3D culture platform. The intensity, however, decays over time due to biodegradation of the substrate. Stability can be improved by introducing fluorinated alkyl silanes to yield hydrophobic paper. This process concomitantly transforms the substrate to a 2D-like scaffold where collagen is predominantly assembled on the surface, thus changing the cellular microenvironment. Altering surface energy also led to fluctuations in collagen intensity and organization over time for smooth (calendered) paper substrates. We infer that the increased roughness improves collagen adsorption through capillary driven petal effect. In general, the influence of the substrate simultaneously affects its ability to host collagen and guide orientation. These findings offer insights into the effects of secondary structures and chemistry of fibrous polymeric materials on cell culture, which we propose as vital parameters when using paper-based platforms.