<p>CFRP is the most popular composite material due to its excellent mechanical properties. Most practical applications of CFRP in various industries require routine machining operations, such as drilling. Delamination of composites during drilling is a critical issue in high-end applications, caused by the thrust force generated throughout the drilling process. In this article, a magnetorheological elastomer (MRE)-based isolator is utilized during the drilling of CFRP to minimize the effects of thrust force. This study considers the impact of fiber orientation; thus, CFRP with unidirectional and bidirectional composites is employed for the drilling operation. An MRE-based isolator can equally reduce the thrust force in both uni-directional and bi-directional CFRP by the same percentage. An empirical model has been developed to explain the variation of thrust force concerning the last five layers of CFRP. The results demonstrate the influence of fiber orientation on magnetic–field induced thrust force. Nonetheless, a significant focus of this work is to elucidate the effect of thrust force reduction through microstructural evaluation of the drilled hole using a scanning electron microscope. Microstructural observations correlate with the analytical findings based on the empirical model. This study includes a layer-wise analysis of the effect of thrust force on drilled hole quality for both types of CFRP.</p>