We study the moduli spaces of k U(N) vortices which are realized by the Higgs branch of a U(k) supersymmetric gauge theory. The theory has 4 supercharges and lives on k D1-branes in a N D3- and NS5-brane background. We realize the vortex moduli space as a C* projection of the vortex master space. The Hilbert series is calculated in order to characterize the algebraic structure of the vortex master space and to identify the precise C* projection. As a result, we are able to fully classify the moduli spaces up to 3 vortices.