It looks like you're always getting rid of the text "MS_FT_" and "_T". If that's true, I'd keep it simple and use the Replace function. Here's how it works.
myString.Replace([Text/variable I'm looking for], [Text/variable to replace it with]);
So you could do something like this...
string[] stringList = { "MS_FT_AL016_T", "MS_FT_NF103_T", "MS_FT_NF109_T", "MS_FT_NF121_T", "MS_FT_NF127_T", "MS_FT_NF128_T", "MS_FT_JMENO_P_T" };
for (int i = 0; i < stringList.Length; i++)
{
stringList[i] = stringList[i].Replace("MS_FT_", "").Replace("_T", "");
Console.WriteLine(stringList[i]);
}
If you're comfortable with Regex, then go ahead with one of the solutions above, but it sounds like you're kinda new to this, so I recommend knowing how it works in order to maintain it. The replace function is about as simple as it gets.