Haskell, <strike>183</strike> 162
=================
<!-- language-all: lang-hs -->

Assuming the file is in <code>file.txt</code>!

    import Data.Char
    import Data.List
    d=drop 1
    main=readFile"file.txt">>=putStr.concat.d.map(d.maximum).transpose.map(group.sort.(++' ':['a'..'z'])).lines.map toLower

If file.txt contains, for example

    abcde
    abcdef
    aaf

The script will output

    aabcdef