In this study, we propose the micro-scale surface functionalization techniques using a maskless, versatile, simple tool, represented by a nano- or micro-capillary atmospheric pressure plasma jet (APPJs). We show the possibility of size-controlled surface functionalization on polymer substrate with amino groups or carboxyl groups by using fluorescent technique. Moreover, we prove the successful connection of biomolecules on the functionalized micro-scale patterns, indicating the possibility to use ultrafine capillary APPJs as versatile tools for biosensing, tissue engineering, and related biomedical applications. With use of this technology, we study the biomolecules patterning onto CNT dot array via ultrafine APPJ for biochip fabrication. An ultrafine APPJ with a micro-capillary was utilized to functionalize amino groups on designated CNT spots. Two-stage plasma treatments, pre-treatment and post-treatment, were conducted to functionalize CNT array by ultrafine APPJ. Biomolecules system, such as biotin-avidin system was employed to assess the feasibility of biomolecule immobilization on CNT. The possibility of this technique for micro-biochip applications was successfully demonstrated by patterning biomolecules onto CNT microarrays.