If you already have a Kindle file, but it’s not formatted right:
Are the first-line indents all wrong?
Does it have uneven spacing?
Are paragraph breaks and page breaks in the wrong places?
Is your Kindle eBook just, in general, messy-looking?
Most of those problems can be fixed quite easily in your MS Word file.
Most of the errors described above are caused when the person who typed your manuscript entered extra spaces and tabs (usually to create first-line indents) and extra paragraph returns, instead of formatting with MS Word Styles.
That’s what MS Word calls “Direct” formatting, and it must be taken out the same way… by hand… using MS Word’s Search and Replace to clean out all those extra spaces and tabs that are causing your Kindle file to look so ragged.