Free energy reconstruction methods such as Gaussian Process Regression (GPR) require Jacobians of the collective variables (CVs), a bottleneck that restricts the use of complex or machine-learned CVs. We introduce a neural network surrogate framework that learns CVs directly from Cartesian coordinates and uses automatic differentiation to provide Jacobians, bypassing analytical forms. On an MgCl2 ion-pairing system, our method achieved high accuracy for both a simple distance CV and a complex coordination-number CV. Moreover, Jacobian errors also followed a near-Gaussian distribution, making them suitable for GPR pipelines. This framework enables gradient-based free energy methods to incorporate complex and machine-learned CVs, broadening the scope of biochemistry and materials simulations.