If you're printing the file, you probably want to use handout mode or article mode.
\documentclass[handout]{beamer}
\usepackage{pgfpages}
\pgfpagesuselayout{2 on 1}[a4paper,border shrink=5mm] % for instance
OR
\documentclass{beamer}
\usepackage{beamerarticle}
If you want pictures of slides, handout mode is best If you want something that looks more like an article, article mode is best. I'll assume you want handout, but the answer is similar for article.
In handout mode, all slides are by default overlayed, which for complicated frames makes a mess. But all of your overlay specifications like <+->
that you used in the beamer .tex file can be specified for the handout mode, too. If there is something you do not want on the handout, add | handout:0
to the overlay specification. So
\only<1-3| handout:0>{foo}
will have foo
appear only on slides 1-3 of the beamer mode and not in the handout. Although it may seem like a pain to deactivate so many specifications in a large beamer file, it's the "right" way to do it because it doesn't change the document in beamer mode (like commenting out would).
See these two questions that relate to making beamers into handouts: