Since diesel is a petroleun product, you will have a hard time getting the smell out. Take all the liners and plastic pieces out of the trunk and throw the carpet away. Then go to Home Depot and get some orange citrus cleaner made by Zep. Then scrub away.

It will eventually go away as long as you stopped the source of the leak.

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1981 300D 147k
1998 VW Jetta Tdi 320k
2001 Dodge Ram 2500 141k
1979 300D 234k (sold)
1984 300D "Astor" 262k(sold)
Mercedes How-To and Repair Pictorials
I love the smell of diesel smoke in my hair