I think it comes from the old 'instead of standing there with your finger up your butt, Do some work!' now shortened to ' pull your finger out...

I think it is out of your rear end.

This is WW2 RAF slang and means nothing in particular while sounding satisfyingly vulgar. It was originally used thus - 'Pull your fingers out chaps, officers approaching!' as a warning to slacking ground crews. 'Pull your finger out and get stuck in', and that it referred to courting couples. http://www.guardian.co.uk/notesandqueries/query/0,5753,-26685,00.html To hurry, to get a move on - During the times of the Men'o'War, when a cannon was loaded, a small amount of powder was poured into the ignition hole near the base of the weapon. In order to keep the powder secure before firing, a crew member pushed one of their fingers into the hole. When the time came for ignition, the crewman was told to pull his finger out. http://www.joe-ks.com/phrases/phrasesP.htm Another way of saying, "Have a go!!" The referee was having a shocker. Someone in the crowd yelled out, "Pull your finger out." http://www.urbandictionary.com/define.php?term=pull+your+finger+out If someone tells you to do this, they want you to hurry up. ('Get your finger out' is also used.) http://www.usingenglish.com/reference/idioms/pull+your+finger+out!.html get/pull your finger out (British & Australian, very informal) if you tell someone to get their finger out, you mean they should start working hard. "You'd better pull your finger out, you should have finished this job hours ago." http://idioms.thefreedictionary.com/get%2Fpull+finger+out http://dictionary.cambridge.org/define.asp?key=finger*8+0&dict=I "take (or pull or get) your finger out": According to "A Dictionary of Catch Phrases American and British," by Eric Partridge, revised by Paul Beale, "take (or pull or get) your finger out" originated about 1930 in the Royal Air Force and was adopted in 1941 or 1942 by the British army. The first edition of Partridge's book had the meaning as "Stop scratching your backside and get on with the job." The revised edition, having been enriched by further scholarship, offers a different meaning as the accurate one. It has to do with couples rather than individuals. To pull your finger out is to hurry, to get a move on. This is another nautical saying and comes from the times of the Men'o'War. When the cannon were loaded a small amount of powder was poured into the ignition hole near the base of the weapon. In order to keep the powder secure before firing, a crew member pushed a finger into the hole. When the time came for ignition, the crewman was told to pull his finger out http://www.phrases.org.uk/bulletin_board/8/messages/178.html

It is generally accepted that the full phrase is Pull your finger out (of your arse) and get a move on! Many slang phrases like this imply some rude undertone in order to make the point. Esoteric theories about canon may have some attraction to psuedo-intellectuals, but the reality is that the vast majority of the population accept its rude, arsehole, context.