how to take system backup

dear all

i am having windows nt network with iis server. while taking backup it’s skips some files those are all running background as a service. how to avoide this. what is the procedure to take system backup. should i stop all the service manually before going to take backup. or is there is any procedure way is available. but i am sure i am running any application while taking backup. i am using nt’s default backup utility. pls. give solutioin.