In this paper we study in detail the post-growth annealing of a copper-containing material deposited with focused electron beam induced deposition (FEBID). The organometallic precursor Cu(II)(hfac)2 was used for deposition and the results were compared to that of compared to earlier experiments with (hfac)Cu(I)(VTMS) and (hfac)Cu(I)(DMB). Transmission electron microscopy revealed the deposition of amorphous material from Cu(II)(hfac)2. In contrast, as-deposited material from (hfac)Cu(I)(VTMS) and (hfac)Cu(I)(DMB) was nano-composite with Cu nanocrystals dispersed in a carbonaceous matrix. After annealing at around 150-200 °C all deposits showed the formation of pure Cu nanocrystals at the outer surface of the initial deposit due to the migration of Cu atoms from the carbonaceous matrix containing the elements carbon, oxygen, and fluorine. Post-irradiation of deposits with 200 keV electrons in a transmission electron microscope favored the formation of Cu nanocrystals within the carbonaceous matrix of freestanding rods and suppressed the formation on their surface. Electrical four-point measurements on FEBID lines from Cu(hfac)2 showed five orders of magnitude improvement in conductivity when being annealed conventionally and by laser-induced heating in the scanning electron microscope chamber.