We present the fabrication of microstructures for photonic and micro-/opto-fluidic applications using femtosecond laser 3D direct writing technique in zirconium-based sol-gel hybrid resist. The advantages and mechanism of photo-polymerization of this new material under fs-pulsed laser exposure are discussed. We suggest and achieve a novel method to fabricate free-standing and movable photonic microstructures, which exhibit much less distortion than the conventional structures attached to substrates, especially when made at close to the photopolymerization threshold. Fabrication of free-movable structures allows us to quantitatively study the shrinkage of photoresist and to improve the resolution. It also contributes to tuning the stop band position of photonic crystals to shorter wavelength. Furthermore, the demonstrated freely-movable property makes it possible to laser trap and manipulate photonic microstructures and have potential application in optofluidics and bio-applications.