Background: Treating extended alveolar defects is challenging for their irregular shape and lack of hard and soft tissues. Virtual planned guided bone regeneration (GBR) with customized meshes aims to optimize the treatment by reducing the risk of dehiscence. The mucosa characteristics are crucial in preserving the bone graft covering and vitality. Methods: Two three-dimensional and extended defects, a mandibular posterior and anterior maxillary atrophy were reconstructed with a particulate graft and a digitally customized scaffold. The workflow entailed merging the pre-operatory clinical related data from intra-oral scanning with the radiologic ones from cone beam-CT. A final ideal prediction of the soft tissue relationship with the implant-borne prosthesis was virtually elaborated, conditioning the design of the titanium membrane fitting the bone defects. Results: A good matching between the scaffold and the bone surface was intra-operatory noted; no complications were registered in the first months of healing with complete integrity of the soft tissues above the graft. Conclusions: A careful evaluation of the soft tissues and a forecast of their final relationship with the implant and prosthesis can improve digital mesh/membrane manufacturing with a suitable healing process up to implant placement and loading, favoring peri-implant tissue stability over time.