After Uribe's victory in the elections, Noguera was appointed Director of the DAS, serving from 2002 to 2005, after which time he was appointed Consul-General if Colombia in Milan in 2006.
On 14 September 2011, the Penal Chamber of the Supreme Court of Colombia found Noguera guilty and sentenced him to 25 years in prison for conspiracy to commit aggravated crime; conspiracy to commit murder; destruction, suppression, and concealment of public documents; and the illegal unauthorized disclosure of secret information and activities, all stemming from his time as Director of the DAS and his involvement in the paramilitary activities of the United Self-Defense Forces of Colombia (AUC) by allowing the DAS to be infiltrated by the AUC.