Fuselage sections of an aircraft are joined using splice elements that compensate for gaps caused by mismatches between mating surfaces on the fuselage sections. The fuselage sections are virtually assembled using computer models that are based on non-contact measurements of as-built fuselage sections. The virtually assembled fuselage sections are used to map the gaps between the mating surfaces. The mapped gaps are used to produce tool inserts having profiles that reflect the dimensions of the gaps. The tool inserts are used to manufacture splice elements having profiles that fill the gaps when the fuselage sections are assembled and joined, thereby eliminating the need for shims and spaces to fill the gaps.