We present the study on the sample transfer characteristics of two different microfluidic interfaces for 2D-CE. These interfaces were manufactured using two different microfabrication technologies: one was obtained via the classical photolithography-wet etching-anodic-bonding process; and the other was obtained via the selective laser-induced etching process. The comparison of the two interfaces, and an intact capillary as a reference, was made via the CE separation of amino acids (arginine and lysine) under different bulk flow conditions, with and without applying bias potential to the secondary channels. The influence on peak shapes, migration times, and repeatabiliy were evaluated.