The amino acid substitution model (matrix) is a crucial part of protein sequence analysis systems. General amino acid substitution models have been estimated from large protein databases, however, they are not specific for influenza viruses. In previous study, we estimated the amino acid substitution model, FLU, for all influenza viruses. Experiments showed that FLU outperformed other models when analyzing influenza protein sequences. Influenza virus genomes consist of different protein types, which are different in both structures and evolutionary processes. Although FLU matrix is specific for influenza viruses, it is still not specific for influenza protein types. Since influenza viruses cause serious problems for both human health and social economics, it is worth to study them as specific as possible. In this paper, we used more than 27 million amino acids to estimate 11 protein type specific models for influenza viruses. Experiments showed that protein type specific models outperformed the FLU model, the best model for influenza viruses. These protein type specific models help researcher to conduct studies on influenza viruses more precisely.