In this study, an algorithm based on conjugate gradient method (CGM) is applied to estimate the unknown time dependent melt depth during laser material processing in liquid phase. The determination of the melt depth is treated as a one-dimensional, transient, inverse heat conduction problem (IHCP). It is assumed that no prior information is available for the functional form of the unknown melt depth, but it can be estimated by an inverse analysis with temperature measurements near the heated surface. The algorithm has been applied to aluminum, titanium and fused quartz and accurate melting depth and temperature distributions can also be returned. In addition, this methodology can also be applied to solve other problems such as calculating the cutting forces in nanomachining by atomic force microscopy (AFM), and estimating the heat sources in a X-ray lithographic process.