As one pronounces 'pre' and 'face' as is done for these as individual words, how come when they form the word 'preface' the pronunciation is so different?
Preface is derived from Old French preface “opening part of sung devotions,” ultimately from Medieval Latin prefatia. It is not derived from the English word face – that's from Old French face and Latin facies “appearance, form, figure.”
That said, even if they were etymologically related, English stems sometimes change pronunciation when you change the word stress (as often happens when adding affixes or changing the part of speech). For example, office has very different vowels from official.
Edit: For a more thorough explanation of this phenomenon, you can read about stress and vowel reduction in English. In words like preface and surface, the stress is on the first syllable, which reduces the vowel of face to a schwa.