Perfect sealing of heterogeneous microstructures in plastic-based microfluidic devices is a significant and urgent challenge to be able to apply them in various microfluidic-based applications, including biosensing, biofiltering, chemical reactors and lab-on-a-chip. In this study we report a simple but practical and effective method to bond a microstructure-incorporated microfluidic device using an ultrasonic bonding method. The specially designed hemisphere-shaped jig, which is called a self-balancing jig, provides a free motion in all x, y, and z directions. These unique properties of the jig allow us to precisely adjust and bond the heterogeneous microstructures in the device. A conventional jig shows in solution leakages around the heterogeneous microstructures while the self-balancing jig did not show any leakages in devices. Furthermore, the bonding performance was also confirmed by using a black ink and fluorescent dye solution. The micro-pillar arrays in the device also demonstrated its capability for selective filtering of microbeads. We believe that this technique would be a useful tool for producing microfluidic devices with heterogeneous microstructures.