A gold-coated array of flow-through inverse pyramids applicable as substrate for entrapment and immobilization of micro-objects and for surface enhanced Raman spectroscopic measurements was fabricated using bulk micromachining techniques from silicon. Surface morphology, optical reflectance, immobilization properties, and surface enhanced Raman amplification of the array were modelled and characterized. It was found that the special perforated periodic 3D structure can be used for parallel particle and cell trapping and highly sensitive molecular analysis of the immobilized objects.