Letters are not generally prefixes. I know of some words (e.g. pseudonym) where you can remove the first letter and it sounds the same, others might have the same meaning.
The English language is very complicated, made more so by the splitting of the language into various sects (e.g. American English, British English). Spelling has evolved over hundreds of years, manipulated by assumptions (e.g. assuming Greek or Roman origins of words), dictionaries being written by people who are not English speakers or familiar with the English language (16th and 17th century and earlier) or a desire to make words more logical for people newly learning the language (modern times), which is further complicated by the fact that spelling reform cannot be done at once as it would cause confusion between words. There are a lot of illogical and unnecessary spelling conventions that are hold overs from older times.
The three most influential spelling texts to this day are as follows:
- Johnson's Dictionary aka A Dictionary of the English Language, circa 1755
- An American Dictionary of the English Language (Noah Webster), circa 1828
- Oxford English Dictionary, circa 1857
More on Spelling and Spelling Reform
The only instance I can think of where a single letter is used as a prefix is a-, which is a negative prefix (e.g. asexual, atheist, apnea).
More on prefixes