This paper reports on the technology development and characterization of polyimide-based, microfluidic channels with integrated nanoporous membranes. A layer transfer and lamination technique is used to fabricate flexible microchannels from spin-on polyimide. The microfluidic channels can be operated at high pressures and flow rates without leakage. Nanopores are created in the polyimide channel walls irradiation with swift heavy ions and subsequent chemical etching of the ion tracks. The irradiation and etching parameters can be used to adjust pore density (by ion fluence) and pore length (via ion energy). The track etching conditions, such as pH-value, concentration, temperature and etch time, define the pore diameter and pore geometry. Typical diameters of cylindrical pores range from 10 nm to 1 or 2 mum. The devices can be used for cross-flow filtration of particles and molecules in fluids or as bioimplants for drug delivery.