In the present study, copper micromolds with a microhole array were precisely manufactured by a synchrotron LIGA process. Like in the traditional LIGA process, a deep X-ray lithography based on a synchrotron radiation was employed as the first manufacturing step. Due to the excellent optical performance of the synchrotron X-ray used, cylindrical micropillar arrays with high aspect ratio could be efficiently obtained. The fabricated microfeatures were then used as a master of the subsequent copper electroforming process, thereby resulting in copper micromolds with a microhole array. Thermoplastic hot embossing experiments with the copper micromolds were carried out for imprinting cylindrical microfeatures onto a polystyrene sheet. Through the hot embossing, the effect of embossing temperature and usefulness of the present manufacturing method could be verified.