I just bought a 12' aluminum V-hull, and am replacing the wood on transom. The piece on outside was too large, so part of the wood was under water. The new piece of plywood I cut was shorter, so it won't be under water anymore. But now I have 2 holes to fill, slightly larger than 1/4". How can I fill them so they won't leak? They are about 3" above the bottom of boat on transom. Thanks.

More than one way to skin that cat.  Nut, bolt and washers on each side all doused in silicone caulk will do it.  Other people will do it other ways.

ss thru bolt w/rubber washer on both sides.

http://www.cabelas.com/cabelas/en/templates/links/link.jsp?id=0001390010655a&type=product&cmCat=SEARCH&returnPage=search-results1.jsp&QueryText=aluminum+boat+repair&N=4887&Ntk=Products&Ntx=mode+matchall&Nty=1&Ntt=aluminum+boat+repair&noImage=0

Thanks guys. If I use the rubber washers, would I still need to use silicone?

The silicon can't hurt and I would use Locktite on the nuts .

You can get a little of this http://www.a1components.com/itemdisplayn.aspx?item=10493

and  http://www.drillspot.com/products/460346/Battalion_1XNB2_Ribbed_Neck_Bolts_and_Nuts

put the tape on both side of the bolt with a locktite nut liek what NJpaulc said.

you can get the tape at HD, Lowe or local hardware store.  I can even send you some if you want for FREE

good luck

Seal it with J-B Weld as you tighten it down.