If you have copied all the files and folders then most can be removed from the my documents folder, however don't delete folders such as my pictures and my videos etc as they are system folders, they're not critical but the operating system will expect them to be there, it's preferable to delete the contents of these folders but leave the folders in place. however this will not make a noticable difference to the performance of the pc, this is a different subject.
to determine whether you have copied all the files; go to my documents, select "select all" from the "edit" menu then right click on the selected files and select "properties" from the menu that appears, this will open a window that will tell you how many files and folders are selected and the total size of them. then do the same on the removable drive, the amount of files and disk space used should be the same.
keep in mind that having a copy of the files on the external drive, i.e. not deleting them from the my documents folder, gives you a very crude sort of backup, if an original is lost you have a copy to replace it, also if the operating system gets corrupt and a re-install is required then you will have saved some data. this is far from ideal but going into backing up data properly is really out of scope, it will also become awkward when you come to copy further files in the future, as some will already exist on the removable drive etc.
if you do copy the files and then delete the originals from the my documents folder; you could consider placing shortcuts into the my documents folder that target the removable drive, this will be useful in scenarios such as saving a new word document using ms word, the "save as" dialogue box will automatically go to the my documents folder, from here you can simply double click the shortcut and it will redirect you to the removable drive, where you can save the document, does this make sense?
windows 2000 includes the NT backup utility which is good for home use, it could be worth your while reading up on using it as you could then be able to create backup archives in a far better manner.
when writing data to external usb drives, ensure that you remove the drive properly when finished, don't just unplug it. when the drive is connected a small icon will appear by the clock, when removing the drive; first click this icon and it will offer you a list of items to safely remove, the drive may be the only one in the list, click the drives entry in the list and wait a short time until the OS states that it can now safely be removed. this isn't very important if you have only read data from the drive, but it's very important if you have written to the drive, to cut a long story short; both the os and the drive have cache mechanisms whereby you save data to a file but it isn't actually written there and then, it can be held in memory, os or drive, and committed later. safely removing a usb drive ensures all data is actually written to the drive before it is removed.