rf plasmas and electrochemical treatments have been used extensively for thin film deposition and etching in the fabrication of microelectronic and photonic devices. These methods can be applied to non-traditional substrates (e.g., paper and stainless steel) to alter surface and bulk properties to create (i) paper-based analytical devices with application to microfluidic devices, and (ii) antibacterial structures on stainless steel. Two examples will be described. First, the effects of plasma-based oxygen etching of cellulose surfaces followed by plasma-enhanced fluorocarbon film deposition will be described and shown to control wetting and adhesion of water droplets. These process steps can also be used to form fully enclosed hydrophilic channels in bulk paper and thereby allow microfluidic device fabrication on inexpensive and renewable substrates. Electrochemical etching of stainless steel creates micro- and nano-structures on stainless steel surfaces that repel water and bacteria. These surfaces have potential applications in orthopedic implants and consumer metal products prone to bacterial contamination.