Do you mean per chromosome or per image? If you want to limit the length of the feature vector you need to define some kind of voting algorithm to decide, which features to use and which ones to neglect. You might prefer the ones that are robust against changes in image quality or which are of most help for separating the different classes in the follow-up classification step. You may post a sample image and a more detailed description of your task to receive answers with more detailed help.

Dear Stephan I mean per chromosome, i have single chromosome images.

i don't want to loose any information extracted like "density profile vector", i fix the size of all feature vectors with longest chromosome length i.e. longest feature vector and replace empty variables by 0, but the results was not so sufficient.