This paper reports a detailed study of the electrical activation and the surface morphology of 4H-SiC implanted with different doping ions (P for n-type doping and Al for p-type doping) and annealed at high temperature (1650–1700 °C) under different surface conditions (with or without a graphite capping layer). The combined use of atomic force microscopy (AFM), transmission electron microscopy (TEM), and scanning capacitance microscopy (SCM) allowed to clarify the crucial role played by the implant damage both in evolution of 4H-SiC surface roughness and in the electrical activation of dopants after annealing. The high density of broken bonds by the implant makes surface atoms highly mobile and a peculiar step bunching on the surface is formed during high temperature annealing. This roughness can be minimized by using a capping layer. Furthermore, residual lattice defects or precipitates were found in high dose implanted layers even after high temperature annealing. Those defects adversely affect the electrical activation, especially in the case of Al implantation. Finally, the electrical properties of Ni and Ti/Al alloy contacts on n-type and p-type implanted regions of 4H-SiC were studied. Ohmic behavior was observed for contacts on the P implanted area, whilst high resistivity was obtained in the Al implanted layer. Results showed a correlation of the electrical behavior of contacts with surface morphology, electrical activation and structural defects in ion-implanted, particularly, Al doped layer of 4H-SiC.