I read the architecture of the model but this is the first time I try to use it . The calculations of the features map will be different if I extract the features from the two last layers or from the last layer but does it will affect if I used it in another model.
Yes it will definitely affect the result. If you are going to use CNN pre-trained models for feature extraction you have to remove the last output layer. Along with that you have to remove all the densely(Fully) connected layers since those will act as ANN for processing to predict the results. We need only the features to be trained using other models like SVC, Random forest etc.