The repeated use of semicritical and critical medical instruments in clinical procedures carries an inherent risk of subsequent patient infection, necessitating "high-level" disinfection or sterilization. However, residual bio-organic contamination may hinder the ability of such processes to efficiently destroy infectious microbes. In this study, the inner surfaces of three clinically used expanded polytetrafluoroethylene endoscope tubes treated with glutaraldehyde disinfectant solutions were analyzed to quantify the efficacy of a buffered peracetic acid sterilization procedure, the STERIS PROCESS, in removing this contamination. Samples of the flexible distal biopsy channel of colonoscope tubes were examined before and after a variable number of STERIS processing cycles by three complementary surface characterization techniques: Fourier transform infrared spectroscopy (FTIR), electron spectroscopy for chemical analysis (ESCA), and atomic force microscopy (AFM). Glutaraldehyde fixed protein deposits identified on the tubing surface decreased with increased STERIS cycles. After 20 STERIS cycles, FTIR data indicated that approximately 30% of the contamination was removed, whereas ESCA indicated that 50% of the contamination was removed. AFM images showed considerable variation between control and processed samples, including evidence for cracks in the residual contamination layer. Clinical glutaraldehyde treatment and subsequent device drying are suggested to be two majors factors that limit effective cleaning of endoscopic tubing.