Development of techniques for joining and welding materials on a micrometer scale is of great importance in a number of applications, including life science, sensing, optoelectronics and MEMS packaging. In this paper, methods of welding and sealing optically transparent materials using a femtosecond fiber laser (1 MHz & 1030 nm) were demonstrated which overcome the limit of small area welding of optical materials from previous work. When fs laser pulses are tightly focused at the interface of the materials, localized heat accumulation based on nonlinear absorption and quenching occur around the focal volume, which melts and resolidifies, thus welds the materials without inserting an intermediate layer.The welding process does not need any preprocessing before the welding. At first, single line welding results with different laser parameters was studied. Then successful bonding between fused silica with multi line scanning method was introduced. Finally, complete sealing of transparent materials with fs laser was demonstrated. Scanning electron microscopy (SEM) images of the sample prove successful welding without voids or cracks. This laser micro-welding technique can be extended to welding of semiconductor materials and has potential for various applications, such as optoelectronic devices and MEMS system.