A flow sensor is provided having a substrate with a sensing element and flow channel aligned over the sensing element. The sensing element senses at least one property of a fluid. The flow channel is aligned by one or more guide elements formed in an alignment layer. The flow channel across the sensing area is accurately and precisely aligned due to the guide elements provided at the wafer-level, facilitating reliable, low-cost, and consistent results among multiple flow sensors. The flow sensor is adapted for use in harsh environments.