Tissue engineering scaffolds with precisely controlled geometries, particularly with surface features smaller than typical cell dimensions (1-10μm), can improve cellular adhesion and functionality. In this paper, soft lithography was used to fabricate polydimethylsiloxane (PDMS) stamps of arrays of parallel 5μm wide, 5μm deep grooves separated by 45 μm ridges, and an orthogonal grid of lines with the same geometry. Several methods were compared for the fabrication of 3-D multi-layer polycaprolactone (PCL) scaffolds with precise features. First, micromolding in capillaries (MIMIC) was used to deliver the polymer into the small grooves by capillarity; however the resultant lines were discontinuous and not able to form complete lines. Second, spin coating and oxygen plasma were combined to build 3-D scaffolds with the line pattern. The resultant scaffolds had good alignment and adhesion between layers; however, the upper layer collapsed due to the poor mechanical rigidity. Finally, a new multi-layer micromolding (MMM) method was developed and successfully applied with the grid pattern to fabricate 3-D scaffolds. Scanning electron microscopy (SEM) characterization showed that the multi-layered scaffolds had high porosity and precisely controlled 3-D structures.