A comparison between two different ways of extracting coherent vortices in three-dimensional (3D) homogeneous isotropic turbulence is performed, using either orthogonal or biorthogonal wavelets. The method is based on a wavelet decomposition of the vorticity field and a subsequent thresholding of the wavelet coefficients. The coherent vorticity is reconstructed from a few strong wavelet coefficients, while the incoherent vorticity is reconstructed from the remaining weak coefficients. The choice of the threshold, which has no adjustable parameters, is motivated for the orthogonal case from the denoising theory. Using only 3 % of the coefficients we show that both decompositions, that is orthogonal and biorthogonal, extract the coherent vortices. They contain most of the energy (around 99 % in both cases) and retain 74 % and 68 % of the enstrophy in the orthogonal and biorthogonal cases, respectively. The incoherent background flow for the orthogonal decomposition, which corresponds to 97 % of the wavelet coefficients, is structureless, decorrelated, and has a Gaussian velocity probability distribution function (PDF). In contrast, for the biorthogonal decomposition, the background flow exhibits quasi-two-dimensional (2D) structures and yields an exponential velocity PDF. Moreover, the biorthogonal decomposition loses 3.7% of both enstrophy and helicity, while they are conserved by the orthogonal decomposition.