You need to use a negative lookahead assertion. From perlre:

(?!pattern)

A zero-width negative lookahead assertion. For example /foo(?!bar)/ ma
+tches any occurrence of ``foo'' that isn't followed by ``bar''.
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However, you can't just add (?!\[) because it will backtrack and match only part of the variable. So to ensure that it will only match the whole variable and not part, add a \b (word boundary): s/(?<!\\)(\$[a-zA-Z0-9_]+)\b(?!\[)/whatever()/ge;