A fuel pre-processing system characterized by: a hydrodesulfurization reactor operating at 200-500 psig (1.38 - 3.45 MPag) and 200-500°C; a sulfur compound absorbing reactor operating at 200-500 psig (1.38 - 3.45 MPag) and 200-400°C; a supply of hydrocarbon fuel containing sulfur bearing material; and a supply of hydrogen at a pressure equal to or greater than the hydrodesulfurization operating pressure; and a sweep separator to provide hydrogen to the fuel pre-processing system; wherein the sweep separator comprises: i) a membrane that is selectively permeable to hydrogen, the membrane including a retentate side and a permeate side; ii) a mixed gas stream including the hydrogen entering the sweep separator and contacting the retentate side of the membrane; iii) at least part of the hydrogen separating from the mixed gas stream and passing through the membrane to the permeate side of the membrane; iv) the mixed gas stream, minus the hydrogen, exiting the sweep separator; v) a sweep gas at high pressure entering the sweep separator and sweeping the hydrogen from the permeate side of the membrane; and vi) a mixture of the sweep gas and the hydrogen exiting the sweep separator at high pressure; vii) the sweep separator thereby separating the selected gas from the gas mixture and pressurizing the selected gas; a reforming reactor; a primary water vaporizer to supply the reforming reactor; a secondary water vaporizer to supply the sweep separator; and, a clean fuel output which is directed to the reforming reactor without being condensed. a hydrodesulfurization reactor operating at 200-500 psig (1.38 - 3.45 MPag) and 200-500°C; a sulfur compound absorbing reactor operating at 200-500 psig (1.38 - 3.45 MPag) and 200-400°C; a supply of hydrocarbon fuel containing sulfur bearing material; and a supply of hydrogen at a pressure equal to or greater than the hydrodesulfurization operating pressure; and a sweep separator to provide hydrogen to the fuel pre-processing system; wherein the sweep separator comprises: i) a membrane that is selectively permeable to hydrogen, the membrane including a retentate side and a permeate side; ii) a mixed gas stream including the hydrogen entering the sweep separator and contacting the retentate side of the membrane; iii) at least part of the hydrogen separating from the mixed gas stream and passing through the membrane to the permeate side of the membrane; iv) the mixed gas stream, minus the hydrogen, exiting the sweep separator; v) a sweep gas at high pressure entering the sweep separator and sweeping the hydrogen from the permeate side of the membrane; and vi) a mixture of the sweep gas and the hydrogen exiting the sweep separator at high pressure; vii) the sweep separator thereby separating the selected gas from the gas mixture and pressurizing the selected gas; i) a membrane that is selectively permeable to hydrogen, the membrane including a retentate side and a permeate side; ii) a mixed gas stream including the hydrogen entering the sweep separator and contacting the retentate side of the membrane; iii) at least part of the hydrogen separating from the mixed gas stream and passing through the membrane to the permeate side of the membrane; iv) the mixed gas stream, minus the hydrogen, exiting the sweep separator; v) a sweep gas at high pressure entering the sweep separator and sweeping the hydrogen from the permeate side of the membrane; and vi) a mixture of the sweep gas and the hydrogen exiting the sweep separator at high pressure; vii) the sweep separator thereby separating the selected gas from the gas mixture and pressurizing the selected gas; a reforming reactor; a primary water vaporizer to supply the reforming reactor; a secondary water vaporizer to supply the sweep separator; and, a clean fuel output which is directed to the reforming reactor without being condensed.