This thesis presents back-end processing steps for polymer labs-on-a-chip which permit the realization of complex applications like biological assays on-chip. Pre-treatment for surface cleaning, hydrophilization to promote capillary action, selective hydrophobization for flow control, dry reagent pre-storage to enable fully integrated chips as well as biocompatible sealing to ensure operation and biological activity after processing are covered. Most of these processing steps are developed on a sample lab-on-a-chip which aims for the on-chip detection of mRNA by nucleic acid sequence based amplification (NASBA) for e.g. cervical cancer diagnostics.