Ion beam sputter deposition (IBSD) techniques for deposition of giant magnetoresistance (GMR) films have been studied using an automated IBSD system designed and built in-house. We have studied the properties of Fe/Cr multilayers deposited using either Ar or Xe ions with the primary ion beam energy varying from 500 eV to 1100 eV. The films were characterized using transmission electron microscopy (TEM), atomic force microscopy (AFM), Auger electron spectroscopy (AES), X-ray photoelectron spectroscopy (XPS), secondary ion mass spectroscopy (SIMS), magnetization measurements, and magnetoresistance measurements. The maximum value of GMR obtained was 49% (measured at 10K). For the Cr spacer thickness layer chosen, this GMR ratio is larger than the values reported for polycrystalline Fe/Cr multilayers deposited by magnetron sputtering. In general, we have found that GMR ratios for the Fe/Cr multilayers increase with decreasing primary ion beam energy, and are greater for films deposited using Xe ions than for films deposited using Ar ions. We explain the observed effects on the basis of energy distributions of sputtered atoms and backscattered working gas atoms (neutrals). The energy distributions were calculated using TRIM (Transport of Ions in Matter) software based on the Monte Carlo method.