Carbon nanotube assemblies can be used for specific applications such as sensors and filters. We present a method and proof-of-concept to directly grow vertically-aligned carbon nanotube structures within sealed enclosures by means of a feedback-controlled laser-assisted chemical vapor deposition technique. The process is compatible with a variety of micro-fabrication processes and bypasses the need for post-process packaging. To further investigate the possibilities of small CNT structures we present a femtosecond laser patterning method. This laser is used to pattern either the catalyst before CNT growth, modifying the surface and catalytic conditions, or the CNT structures directly after growth. © 2014 SPIE.