Fused deposition modeling represents a flexible and relatively inexpensive alternative for the production of custom-made polymer lattices. However, its limited accuracy and resolution lead to geometric irregularities and poor mechanical properties when compared with the digital design. Although the link between geometric features and mechanical properties of lattices has been studied extensively, the role of manufacturing parameters has received little attention. Additionally, as the size of cells/struts nears the accuracy limit of the manufacturing process, the interaction between geometry and manufacturing parameters could be decisive. Hence, the influence of three geometric and two manufacturing parameters on the mechanical behavior was evaluated using a fractional factorial design of experiments. The compressive behavior of two miniature lattice structures, the truncated octahedron and cubic diamond, was evaluated, and multilinear regression models for the elastic modulus and plateau stress were developed. Cell size, unit cell type, and strut diameter had the largest impact on the mechanical properties, while the influence of feedstock material and layer thickness was very limited. Models based on factorial design, although limited in scope, could be an effective tool for the design of customized lattice structures.