Microfluidic paper based analytical devices (μ-PADs) have shown promising results for disease diagnostics in resource limited settings but they often lack effective fluid flow control in the hydrophilic channels. Flow control in μ-PADs is necessary to conduct multiple step assays with minimum user interference. Using fluorocarbon (pentafluoroethane) plasma deposition followed by O2 plasma etching with a metal mask, flow control functionality in fully enclosed channels was achieved. Channels with up to a 10-fold difference in wicking rate were fabricated by changing the O2 plasma etch time. Metal meshes were used to locally vary the O2 plasma etch rate and therefore fabricate channels with different wettability inside a single paper substrate in a single etch step. The channels in fully enclosed devices are isolated, thereby preventing contamination due to handling and environmental exposure. To gain additional reliability, channels were covered with non-porous adhesive tape to minimize the effect of evaporation on fluid flow to eliminate variation in device operation under different humidity conditions. Proof of concept was demonstrated by fabricating and operating a device with three channels that converged to a single reaction zone. Solutions of different pH values were sequentially transported to and reacted with an indicator deposited at the reaction zone. μ-PADs fabricated by this method are suitable for field use when conducting complex low-cost diagnostic tests.