base64 -d will do what you want out of the box on my system:

$ echo one | base64  > file.txt
$ echo two | base64  >> file.txt
$ echo three | base64  >> file.txt

$ cat file.txt 
b25lCg==
dHdvCg==
dGhyZWUK

$ cat file.txt | base64 -d
one
two
three
$

Alternatively, using the highest voted bash for-line-in-file pattern:

$ cat file.txt | while read line ; do
    echo "$line" | base64 -d ; 
done

Will result in the same:

one
two
three