A method and system for providing a fluidic interface to slides bearing microarrays of biomolecules or other samples immobilized thereon to perform a variety of chemical reactions or processing steps on the slide. An interface device seals against the slide to form a chamber or chambers containing all or a portion of the microarray, providing selective access to portions of the slide. The interface device includes inlet and outlet ports permitting liquid sample and reagents to be introduced to and removed from the chamber accessing the slide surface. Pre- and post-array microfluidic circuitry may be included in the interface device or in attachable modules. The system may include one or more compartments for collecting and storing waste fluids.