Transmission electronic microscopy (TEM) and ultraviolet-visible absorption spectroscopy were used to characterize several silver and copper sols employed as substrates in surface enhanced Raman spectroscopy(SERS). In this study we have focused our attention on the changes observed when the large scale roughness is modified by the aggregation agent 1,5-dimethylcytosine (DMC). A previous analysis of several unaggregated silver and copper colloids and a comparison with the corresponding aggregated colloids were made, so that a relationship between the morphology of the aggregates and the SERS results was obtained. Information about the aggregation process of the colloids studied is also presented, on the basis of the results obtained from TEM, UV-visible spectroscopy, and the study of the variation of the SERS signal with the concentration of DMC. From these results, the morphology of the resulting aggregates which yields the most intense SERS signal is inferred. A different aggregation mechanism is suggested for each colloidal metal, according to the remarkably different geometry of the final aggregates observed. This is further attributed to the different sizes of the simple particles present in the original colloids.