the tokenizer splits a character stream into words, which are the atomic units of search. strings can be split based on whitespace, word boundaries, etc. these words are often passed through filters in the second stage which apply additional transformations to the words (like soundex codes, porter stemming, etc). the result is a normalized representation of the words that can be efficiently compared.
for example: "The Cats Eat Cheese!" might be normalized to the words: 1) cat 2) eat 3) cheese
"the" was removed (stopword), cat is now singular (stemming), punctuation is gone, and the words are lower cased.