I want to copy my windows dir, including sub dir's hidden files & system files to a back up drive that I can use to boot with if need be. I do not want to copy any program files!
I can I do this without getting " File in use, cnnot copy" error.
copy command in DOS won't copy sub dir's and xcopy won't copy hidden or system files.

XCOPY C:\WINDWOS :\WINDOWS /S/E

will copy all subdirectories under Windows, including empty ones. I don't think that Windows has any hidden files unless you made them that way.
You could always use the Backup command that comnes with DOS or Win95 (in GUI form only) to creat archives of the files, but that won;t copy hidden files either.

I don't think it can be done. DR-DOS will copy hidden files, and, if you boot with it, there is no file sharing problem. The problem is long filenames. You have to copy them from inside windows. There are programs on the market that will do this; however, here again there is a problem. Windows ME and later will not allow all the files to copy.

try this, not sure if it will work exactly to your specifications--do it in this order:
cd windows
attrib -h *.* (removes hidden attribute)
xcopy c:\windows /e/s z: where z is the drive letter of where you want it copied (destination)
attrib +h *.* (restores hidden attribute)
Do the above command on c:\windows and the destination drive.

Is there any option in XCOPY where i can copy files not existing in destination. It should not prompt or overwrite the existing files.

I found this little trick some years ago, and so far in building a lot of new systems for friends and customers, this has about a 95% success rate if the new drive will be used on the EXISITING PC. Trying to use this to put data on a new larger drive that will then go into a NEW system has about a 10% success rate, as Windows and the existing registry will find itself allocating resources for devices and programs that can't be used.

Here's whatcha do:

Have a "donor" PC that has a good working Windows 9x OS on it. Hook the NEW drive and the old drive to it as Master & Slave on the SECONDARY IDE channel.

Start Windows on the "donor" PC.

Go to a DOS box [START, RUN, COMMAND]

Assuming the NEW drive is fdisked and formatted and is the D: drive and the old drive is E:, you'll type this at the
C:> prompt...

xcopy e:\ d:\ /e/c/h/k/-y

and hit ENTER. This will copy EVERYTHING, with any attribute, intact to the new drive.
Essentially a DOS version of ghosting.

When this finishes, put the NEW drive as Primary Master into the old PC and use a boot floppy to run FDISK and set the partition to ACTIVE if you haven't done so already. Reboot and VIOLA! :)

Hope that helps...

Danno