Yes, this is possible, but requires a few preparations.
Open Advanced - Settings/Configuration - Editor - Advanced and check the setting Allow editing of text files with hex 00's without converting them to spaces. This is necessary because otherwise UltraEdit would replace each null byte by a space character after replacing base64 encoded data with decoded data.
Open a new ANSI file and copy and paste into this file just the base64 encoded data. It is important that the new file is not a Unicode file (UTF-16, UTF-8), but a 1 byte per character encoded text file not containing anything else than the base64 encoded data.
Press Ctrl+A to select all and use command Decode Base64.
The selected base64 encoded data is replaced by decoded binary data displayed in text editing mode.
Press F12 to open Save As dialog and save the new file with name and extension suitable for the decoded data.
I verified the steps posted here with a PDF file with 1.499.046 bytes stored base64 encoded in a generic mbox file (mail format) for which I had also the original PDF file for a binary comparison after decoding the data.