We report a novel method to fabricate high quality 2-inch freestanding GaN substrate grown on cross-stacked carbon nanotubes (CSCNTs) coated sapphire by hydride vapor phase epitaxy (HVPE). As nanoscale masks, these CSCNTs can help weaken the interface connection and release the compressive stress by forming voids during fast coalescence and also block the propagation of threading dislocations (TDs). During the cool-down process, thermal stress-induced cracks are initiated at the CSCNTs interface with the help of air voids and propagated all over the films which leads to full self-separation of FS-GaN substrate. Raman and photoluminescence spectra further reveal the stress relief and crystalline improvement of GaN with CSCNTs. It is expected that the efficient, low cost and mass-producible technique may enable new applications for CNTs in nitride optoelectronic fields.