We calculate the structure of individual vortices in rapidly rotating Bose-Einstein condensates in a transverse harmonic trap. Making a Wigner-Seitz approximation for the unit cell of the vortex lattice, we derive the Gross-Pitaevskii equation for the condensate wave function in each cell of the lattice, including effects of varying coarse grained density. We calculate the Abrikosov parameter, the fractional core area, and the energy of individual cells.