Due to affordability, and the ability to parametrically control the vital processing parameters, material extrusion is a widely accepted technology in tissue engineering. Material extrusion offers sufficient control over pore size, geometry, and spatial distribution, and can also yield different levels of in-process crystallinity in the resulting matrix. In this study, an empirical model based on four process parameters—extruder temperature, extrusion speed, layer thickness, and build plate temperature—was used to control the level of in-process crystallinity of polylactic acid (PLA) scaffolds. Two sets of scaffolds were fabricated, with low- and high-crystallinity content, and subsequently seeded with human mesenchymal stromal cells (hMSC). The biochemical activity of hMSC cells was tested by examining the DNA content, lactate dehydrogenase (LDH) activity, and alkaline phosphatase (ALP) tests. The results of this 21-day in vitro experiment showed that high level crystallinity scaffolds performed significantly better in terms of cell response. Follow-up tests revealed that the two types of scaffolds were equivalent in terms of hydrophobicity, and module of elasticity. However, detailed examination of their micro- and nanosurface topographic features revealed that the higher crystallinity scaffolds featured pronounced nonuniformity and a larger number of summits per sampling area, which was the main contributor to a significantly better cell response.