CO is one of the most abundant molecules in protoplanetary disks, and optically thin emission from its isotopologues has been detected in many of them. However, several past works have argued that reproducing their relatively low emission requires a very low disk mass or significant CO depletion. Here, we present MINT, a tool to estimate disk masses with CO isotopologues. It includes isotope-selective chemistry, a density and temperature structure consistent with thermal pressure gradient, and includes CO conversion to CO2 ice onto grains.The code uses an SED-derived dust disk structure on top of which it builds a self-consistent gas distribution. We also show an application of MINT on the disk of RU Lup, a high-accreting star whose disk was previously inferred to have a gas mass of only ~1.5 × 10-3 M⊙ and gas-to-dust mass ratio of ~4. Our best-fit SED model to the long-wavelength continuum emission can explain the total C18O luminosity, as well as the C18O velocity and radial profiles with a gas mass that is an order of magnitude higher, ~1 × 10-2 M⊙. The code for generating self-consistent vertical hydrostatic equilibrium disk models with SED fitting built on RADMC-3D, LIME and a reduced chemical network will also be released.