Microfluidic devices play a crucial role in advanced cell biology applications, including cell separations, cultivations, migration and interaction studies, diagnostic devices, and organ‐on‐chips. One of the frequent purposes of such devices is the ability to selectively address the attachment of cells at defined locations on the surface. This study explores the application of middle‐energy carbon, oxygen, and nitrogen ions to locally modify the surface of cyclic olefin copolymer (COC) thermoplastic material, allowing selective cell growth on patterned polymer surfaces. The investigation considers ion element type, ion beam energy, and ion irradiation fluence, analyzing their influence on the modification effect. Characterization of the modified surfaces involves various surface‐analytical methods such as contact angle, energy dispersive spectroscopy (SEM‐EDX), atomic force microscopy (AFM), x‐ray photoelectron spectroscopy (XPS), rutherford backscattering spectrometry (RBS), and elastic recoil detection analysis (ERDA). The study extends to practical aspects, with a representative cancer cell line, MCF‐7, grown on the patterned surface to evaluate the degree of selective attachment. Additionally, the stability of the irradiated patterns is tested under elevated temperatures beyond the glass transition temperature (Tg), demonstrating the compatibility of the approach with hot embossing technology. The findings underscore the potential of ion beam treatment for COC in cell‐biology‐related applications, offering insights into surface modification techniques for enhanced functionality in microfluidic devices.