The use of bottom-up approaches in tissue engineering applications is advantageous since they enable the combination of various layers that could be made from different materials and/or incorporate different biochemical cues. Regarding the complex structure and the vascular system of the bone tissue, the aim of this study was to develop an innovative bottom-up approach that allows the construction of 3D biodegradable scaffolds from 2D microfabricated membranes with precise shape, pore size and porosity. For that purpose, poly (caprolactone) (PCL) and starch – poly (caprolactone) (SPCL (30% starch)) blended sheets were used as substrates to produce the microfabricated membranes using micro hot-embossing. The use of this micro fabrication process allowed accurately imprinting micropillars and microholes in reproducible way. The assembling of the microfabricated membranes was performed using an easy, highly reproducible and inexpensive approach based on its successive stacking. Additionaly, the suitability of the microfabricated membranes to support the attachment and the cytoskeletal organization of human bone marrow stem cells (hBMSCs), macrovascular endothelial cells and osteoblasts derived from hBMSCs was demonstrated. Furthermore, hBMSCs proliferated and maintained the expression of the stromal progenitor marker STRO-1 when cultured on both PCL and SPCL microfabricated membranes. The proposed methodology constitutes a promising alternative to the traditional processing methods used to prepare tissue engineering scaffolds.