This paper presents a detailed analysis of synchronization methods based on scattered pilots for filter bank based multicarrier (FBMC) communications, taking into account the interplay of the synchronization, channel estimation, and equalization methods. We show that by applying pilots designed specifically for filter banks, the carrier frequency offset (CFO), fractional time delay (FTD), and channel response can be accurately estimated. Further, a novel joint FTD and channel estimation scheme, based on iterative interference cancelation, permits extending the FTD estimation range well beyond the limit imposed by the pilot separation. The channel parameter estimation and compensation are successfully performed totally in the frequency domain, in a subchannel-wise fashion, which is appealing in spectrally agile and cognitive radio scenarios. The performance evaluation is done in a hypothetical WiMAX scenario in which an FBMC system would substitute OFDM maintaining as much physical layer compatibility as possible.