Police had named Top as the prime suspect in the bomb plot, as well as a series of other attacks, including the 2002 nightclub bombings in Bali which killed more than 202 people, mostly foreign tourists.
Born in Malaysia he had headed a splinter network of the Jemaah Islamiyah, a group believed to have ties to al-Qaeda fighting for an Islamic state.
In a 2005 video, Top claimed to be al-Qaeda's representative in Southeast Asia and to be carrying out attacks on Western civilians to avenge Muslim deaths in Afghanistan.
Following his death last month, Sidney Jones, a senior adviser with the International Crisis Group think tank, told Al Jazeera that Indonesian officials were confident that Top's killing would make "a major dent in Indonesia's terrorist networks".
"He was very clearly trying to be an Indonesian replica of Osama bin Laden. He was the one major terrorist in Indonesia who was following Bin Laden's directive of working to wage war on America and its allies wherever possible."