A new approach is presented to improve the spatial and temporal resolution of the Vertical Total Electron Content (VTEC) estimates for regional positioning applications. The proposed technique utilises a priori information from the Global Ionosphere Maps (GIMs) of the Center for Orbit Determination in Europe (CODE), provided in terms of Spherical Harmonic (SH) coefficients of up to degree and order 15. Then, it updates the VTEC estimates using a new set of base-functions (with better resolution than SHs) while using the measurements of a regional GNSS network. To achieve the highest accuracy possible, our implementation is based on a transformation of the GIM/CODE VTECs to their equivalent coefficients in terms of (spherical) Slepian functions. These functions are band-limited and reflect the majority of signal energy inside an arbitrarily defined region, yet their orthogonal property is remained. Then, new dual-frequency GNSS measurements are introduced to a Least Squares (LS) updating step that modifies the Slepian VTEC coefficients within the region of interest. Numerical application of this study is demonstrated using a synthetic example and ground-based GPS data in South America. The results are also validated against the VTEC estimations derived from independent GPS stations (that are not used in the modelling), and the VTEC products of international centres. Our results indicate that, by using 62 GPS stations in South America, the ionospheric delay estimation can be considerably improved. For example, using the new VTEC estimates in a Precise Point Positioning (PPP) experiment improved the positioning accuracy compared to the usage of GIM/CODE and Klobuchar models. The reductions in the root mean squared of errors were ∼23% and 25% for a day with moderate solar activity while 26% and ∼35% for a day with high solar activity, respectively.