To archive an item from the system, double-click into it on the Stock screen. The window below will appear.
Tick the box called "Archived" in the middle section of the window. When you press Save, this will now have disappeared from the Stock screen, unless Show Archived is ticked.
Also...
On the front page of stock, with a stock item selected from the list, click Archive to archive the Selected Items or All Items with zero quantity. This is shown below: