 Federer also took four ATP Masters Series 1000 wins : Indian Wells , Miami , and Cincinnati on hard court , and Hamburg on clay . The win in Miami was particularly noteworthy as it was the first final contested between Federer and Rafael Nadal in what would become one of the greatest rivalries in tennis history . Federer received from down two sets and a break to take the final in five sets . Furthermore , Federer won two ATP 500 series events at Rotterdam and Dubai . Federer lost the year @-@ end championships to David Nalbandian in five sets while playing through a foot injury that sidelined him for almost the entire season after September . He maintained his position as world No. 1 for the entirety of the season . 
