I'm about to design a brand mark for an engineering company, the first letter of the company name being "E" and I want to manipulate this character like a sigma "Σ" letter, but need to make sure it's will be fine.
Yes you can.
The Greek alphabet is merely an alphabet. Using a drawing which is representative of the Sigma glyph is no different than using a drawing representing the E glyph from a Latin alphabet or any glyph from any alphabet.
The concept or idea of a glyph can not be copyrighted. You are free to draw your own glyph which resembles the Greek sigma glyph.
Only how a glyph has been implemented could be seen as a "creative work" and therefore copyrightable. As long as you aren't replicating some specific rendition of the sigma glyph, you are fine. And, in many instances, commercial fonts which contain the sigma glyph may be fine to use. However, you would need to check any licensing before using the sigma glyph from a particular font or typeface.