The thermal fluctuations and disorder of vortices structure in highly anisotropic layered type II superconductors has been studied by Monte Carlo simulation in two dimensional Ginzburg-Landau model with the quasi-momentum basis. Vortices structure are studied with disorder parameter ζ=0~1 and reduced temperature a_T=-17~-11 in the thesis. I developed the rotation averaging to analysis the snapshots of the Fourier transform of the superfluid density. I identified the melting line with disorder by comparing the vortices structure in pure system that the melting point of finite sample has been developed by Y. Kato and N. Nagaosa. And I identified the glass (irreversibility) line by comparing the difference of vortices structure with two different distribution of disorder. One can see the vortices pin on the disorder with disorder strong enough so that there are difference between the vortices structure with two different distribution of disorder to find the glass transition line. I will give a a_T-ζ phase diagram in the end.