We studied the thermally induced phase transformations of electron-beam-induced deposited (EBID) amorphous carbon nanostructures by correlating the changes in its morphology with internal microstructure by using combined atomic force microscopy (AFM) and high resolution confocal Raman microscopy. These carbon deposits can be used to create heterogeneous junctions in electronic devices commonly known as carbon-metal interconnects. We compared two basic shapes of EBID deposits: dots/pillars with widths from 50 to 600 nm and heights from 50 to 500 nm and lines with variable heights from 10 to 150 nm but having a constant length of 6 μm. We observed that during thermal annealing, the nanoscale amorphous deposits go through multistage transformation including dehydration and stress-relaxation around 150 °C, dehydrogenation within 150-300 °C, followed by graphitization (>350 °C) and formation of nanocrystalline, highly densified graphitic deposits around 450 °C. The later stage of transformation occurs well below commonly observed graphitization for bulk carbon (600-800 °C). It was observed that the shape of the deposits contribute significantly to the phase transformations. We suggested that this difference is controlled by different contributions from interfacial footprints area. Moreover, the rate of graphitization was different for deposits of different shapes with the lines showing a much stronger dependence of its structure on the density than the dots.