Использование Apache Commons
String filePath = "/apps/fraud";
String[] acceptedExtension = {"ctl","otl","dat","csv","xls"};
String[] acceptedFolders = {"suresh","dir","kernel"};
Collection fileList = FileUtils.listFiles(
new File(filePath),
new SuffixFileFilter(acceptedExtension) ,
new NameFileFilter(acceptedFolders)
);