The effect of the reduction of the magnetic layer thickness on sample correlated roughness in Co/Cu granular samples produced via the incomplete layer method has been investigated. When Co layer thickness is smaller than 3 angstrom, they undergo a fragmentation process that modifies the expected sample magnetic and magnetoresistive properties. This behavior has been studied with anomalous x-ray diffuse intensity data collected in grazing incidence configuration by evaluating both roughness correlation lengths and the dynamic roughness exponent. The fragmentation process is found to promote conformal nanoscale roughness and to lower the giant magnetoresistance response of the system. (C) 2008 American Institute of Physics.