A preparative scale free-flow isoelectric focusing (FF-IEF) device is developed and characterized with the aim of addressing needs of molecular biologists working with protein samples on the milligrams and milliliters scale. A triangular-shape separation channel facilitates the establishment of the pH gradient with a corresponding increase in separation efficiency and decrease in focusing time compared to that in a regular rectangular channel. Functionalized, ion-permeable poly (acrylamide) gel membranes are sandwiched between poly (dimethyl silxoane) (PDMS) and glass layers to both isolate the electrode buffers from the central separation channel and also to selectively adjust the voltage efficiency across separation channel to achieve high electric field separation. The 50 × 70 mm device is fabricated by soft lithography and has 24 outlets evenly spaced across a pH gradient between pH 4 and 10. This preparative FF-IEF system is investigated and optimized for both aqueous and denaturing conditions with respect to the electric field and potential efficiency and with consideration of Joule-heating removal. Energy distribution across the functionalized polyacrylamide gel is investigated and controlled to adjust the potential efficiency between 15 - 80% across the triangular separation channel. The device is able to achieve constant electric fields high as 370 ± 20 V/cm through the entire triangular channel given the separation voltage of 1800 V, enabling separation of five fluorescent pI markers as a demonstration example.