You need to customize file upload dialog in that case. These are the paths under your alfresco installation you need to look into. <ALF_HOME>\tomcat\webapps\share\WEB-INF\classes\alfresco\site-webscripts\org\alfresco\components\upload <ALF_HOME>\tomcat\webapps\share\components\upload
I tried to customize, but I couldn't find ways to avoid specified content types like exe or msi files.Can you please tell me which all are the files i have to modify and how to modify