Abstract-Flow-induced Molecular Communication (FMC), where molecular transport is performed via flow, is utilized in microfluidic channels to enhance diffusion-based molecular communication. The incorporation of the microfluidic channel and the transport of molecules by flow, i.e., convection, require a rigorous analysis to develop an end-to-end concentration propagation model and a design for microfluidic channels. To the best of our knowledge, this is the first attempt to analyze concentration propagation in microfluidic channels from FMC perspective and devise them specifically to enhance the FMC. In this paper, a system-theoretic analysis of molecular transport is presented first. The system-theoretic model incorporates the solution of flow velocity in microfluidic channels and yields an end-to-end transfer function for concentration propagation based on building blocks of microfluidic channels. Then, the design of microfluidic channels is performed based on the least-squares Finite Impulse Response (FIR) filtering to achieve the desired end-to-end transfer function in FMC. According to the desired pass and stop bands, the required length and aspect-ratio parameters of the microfluidic channels are obtained for FIR filtering. The transfer functions for FMC is elaborated via numerical results. Furthermore, two example designs of microfluidic channels are presented for least-squares FIR band-pass and band-stop filtering in FMC.