In electron probe beam micro-analysis (EPMA), the electron accelerating voltage decides the penetration depth of the probe beam therefore the voltage dependence of the characteristic X-ray emission intensities reflects the composition depth distribution. This effect can be utilized to determine an accurate composition value for the matrix and to identify other phases. As the measured emission intensity is a convolution of the entire probed depth, a parameter fitting procedures using a computer was developed to deconvolute measured spectra of accelerating voltage dependent data. Using this method, a surface phase segregated on CuGaSe2 epi-layers grown by molecular-beam epitaxy under Cu-excess conditions was detected and found to be Cu3Se2. Oxidation of CuInSe2 or CuGaSe2 film surfaces was also detected by EPMA. The thickness of the natural oxide layers evaluated by this technique was several nanometers. The weakest point in EPMA analysis is its sensitivity to specimen surface roughness. A theoretical estimation of surface roughness effects matched actual data well. This result suggests possible corrections for measured values on rough surfaces. (C) 2003 Elsevier Science B.V. All fights reserved.