Free-flow counterflow gradient focusing (FF-CGF) is a promising tool for protein fractionation. This work establishes guidelines to construct an FF-CGF system suitable for preparative applications. Numerical and analytical computations are undertaken to investigate design parameters, including device geometry, flow conditions, sample concentration, and applied voltage. This collective information serves as a design tool to guide the fabrication of the device, which, in this case, is constructed from polymethyl methacrylate (PMMA) and double-sided tape. Furthermore, the design tool also supports device operation and provides insights into the expected resolution and throughput. Experimental results, which demonstrated the ability of the designed chip to generate a uniform counterflow gradient while separating small molecules and proteins, validated the accuracy of the design guidelines.