Thin film materials are widely used in the fabrication of semiconductor microelectronic devices. In thin film deposition, cleanliness of substrate surface have become critically important as over 50% of yield losses in integrated circuit fabrication are caused by microcontamination [1]. There are many wafer cleaning techniques. The most successful approach for silicon wafer cleaning technique is RCA clean [2]. But for glass substrate it is still not known which procedure of cleaning is the best. This paper provides an understanding of the right way of glass wafer cleaning method, with a focus towards identifying good bond strength. Two wafer cleaning techniques have been used for cleaning glass substrates in the context of laser micro-joining of dissimilar substrates. First cleaning procedure involves two steps, first cleaning in acetone solution and then in DI water solution. After each step dried with N-2. Second cleaning procedure involves four steps, first cleaning with 1% Alconox solution, second in DI water, third in acetone solution and finally in a methanol solution and dried with N-2 after each step. Deposition of Ti thin film on top of these two types of substrate using DC magnetron sputtering method also showed better adhesion of Ti film on glass for the second type of cleaning method. Scanning electron microscopy (SEM) analyses of the lap shear tested failed surfaces for these two kinds of samples revealed strong bond for samples prepared by second cleaning method compared to first cleaning method. Characterization of these two sets of samples using X-ray photoelectron spectroscopy (XPS) has shown excellent contamination removal for the second cleaning method. This modification is believed to be due to reduction of carbon contamination. (C) 2011 Elsevier B. V. All rights reserved.