Recently, confusion network decoding has been applied in machine translation system combination. Due to errors in the hypothesis alignment, decoding may result in ungrammatical combination outputs. This paper describes an improved confusion network based method to combine outputs from multiple MT systems. In this approach, arbitrary features may be added log-linearly into the objective function, thus allowing language model expansion and re-scoring. Also, a novel method to automatically select the hypothesis which other hypotheses are aligned against is proposed. .