Methods and apparatuses are provided for extraction and collection of sets of one or more cells from a formalin-fixed paraffin embedded tissue sample. A laser is used to remove sets of one or more cells from an immobilized sample within a microfluidic device, and a fluid flow element washes the removed set of one or more cells away from the immobilized sample, preferably to be collected in a downstream sample collection device. Morphological and/or positional information may be preserved to permit at least one technique (e.g., amplification, sequencing, and/or analytical, optionally performed after cells are lysed downstream of the microfluidic device) to be related to the original spatial location of the set of one or more cells in the immobilized sample.