In this paper, a new channel estimator for optical filter bank multicarrier with an offset-QAM modulation (FBMC/OQAM) system is proposed. The conventional channel estimation techniques that are based on interference approximation method (IAM) preamble with least squares (LS) approach suffers from sensitivity to intrinsic imaginary interference (IMI). Therefore, a filterbank-assisted (FB) technique is proposed to eliminate the residual interference associated with the preamble to improve the performance of optical FBMC/OQAM system. To further enhance the system performance, a thresholding block is added between the synthesis and analysis filter banks at the receiver to suppress the residual interference. Simulation findings show that the proposed channel estimator is more effective than the conventional IAM-R and IAM-C with LS based channel estimation at estimating the optical channel that includes chromatic dispersion and residual IMI.