In order to improve the efficiency of ultrasonic bonding process for a polymer Electro-Mechanical System(MEMS) and to prevent the flow of polymer under a high temperature,a micro energy director array was proposed. Based on the experiment of PMMA micro-pipe sealing, the influence of micro energy director array on the process of ultrasonic sealing was studied. Five kinds of micro energy directors with different heights were fabricated on the sealing surface by a hot embossing technique. The method of ultrasonic precise sealing based on acoustic transfer efficiency feedback was used in the experiment to study the influence of the height of the micro-array structure on the quality of ultrasonic sealing and to observe the wetting behavior of micro-array structure. Experimental results indicate that the ultrasonic energy to achieve complete connection increases with increasing the height of micro energy director array. The micro energy director can control the flow of the melting-polymer effectively and can obtain the uniform sealing surface and high quality precise sealing.