Boxcars were secured with serialized seals. Each consisted of a metal strap with a one time fastener, either a metal ball with a catch inside and a hook on the other end that can be entered only once and never removed without destroying the seal, or a soft lead rivet on one end and a hole on the other which was riveted closed. Think of it like a cable tie only more secure. These are the types I have seen. RGS and D&RGW used the former and C&S used the latter. The ball latch type had embossed letters "D&RGW" or "RGS" and then a unique serial number. The rivet type had printed letters and numbers "C&S" then the serial number.
The seals were wrapped through the latch on the car doors (all three, rembember the lumber door in the end) and all of the seal numbers were recorded on the shipping invoices and records. If the seals didn't match or were broken you would inventory the contents. Once delivered the consignee would break the seals and discard them.
I'm not sure what is currently in use.