In this paper, we present a focused femtosecond laser Bessel beam scanning technique for the rapid fabrication of large-area 3D complex microtube arrays. The femtosecond laser beam is converted into several Bessel beams by two-dimensional phase modulation using a spatial light modulator. By scanning the focused Bessel beam along a designed route, microtubes with variable size and flexible geometry are rapidly fabricated by two-photon polymerization. The fabrication time is reduced by two orders of magnitude in comparison with conventional point-to-point scanning. Moreover, we construct an effective microoperating system for single cell manipulation using microtube arrays, and demonstrate its use in the capture, transfer, and release of embryonic fibroblast mouse cells as well as human breast cancer cells. The new fabrication strategy provides a novel method for the rapid fabrication of functional devices using a flexibly tailored laser beam.