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Estimates of the past thermal state of the land surface are crucial to assess the magnitude of current anthropogenic climate change, as well as to assess the ability of Earth System Models to forecast the evolution of the climate near the ground, not included in standard meteorological records. Subsurface temperature data are able to retrieve long-term changes in surface energy balance -from decadal to millennial time scales, thus constituting an important record of the dynamics of the climate system that contributes low-frequency information to proxy-based paleoclimatic reconstructions. A broadly used technique to retrieve past temperature and heat flux histories from subsurface temperature profiles based on a Singular Value Decomposition (SVD) algorithm was able to take into account a limited number of sources of uncertainty, with recent works attempting to increase the number of factors considered in uncertainty estimates. Nevertheless, the SVD methodology did not define a statistical framework for aggregating inversions of individual profiles to derive global results, which lead to estimates of global and regional uncertainties that are difficult to interpret. To alleviate the lack of a conceptual framework for estimating uncertainties in past temperature and heat flux histories at regional and global scales, we combine a new bootstrapping sampling strategy with the broadly used SVD algorithm, and assess its performance against the original SVD technique and another technique based on generating perturbed parameter ensembles of inversions. The new bootstrap approach is able to reproduce the prescribed surface temperature series used to derive an artificial profile. Bootstrap results are also in agreement with the global mean surface temperature history and the global mean heat flux history retrieved in previous studies. Furthermore, the new bootstrap technique provides with a meaningful uncertainty range for the inversion of large sets of subsurface temperature profiles. We suggest the use of this new approach particularly for aggregating results from a number of individual profiles, and to this end, we release the programs used to derive all inversions in this study as a suite of codes labelled CIBOR 1.0: Codes for Inverting BORholes, version 1.0. [ABSTRACT FROM AUTHOR]