try this (updated):

use strict;
use warnings;
use Text::CSV;
use MIME::Base64;

my $i=0;

my @columns;
my @cleanData;
my @input;

my $file = 'data.csv';

my $csv = Text::CSV->new();


my $string;


while (<DATA>) {
    
    if ($csv->parse($_)) {
        my @values = $csv->fields();
        push @cleanData, \@values;
    } else {
        my $err = $csv->error_input;
        print "Failed to parse line: $err";
    }
}

open (MYFILE, ">", "output.csv") or die $!;
    
for my $column (@cleanData){
        foreach my $value (@{$column}) {
            chomp $value;
            $value = check($value);
        }
    print MYFILE join(',', @$column), "\n";    
    }
   
close MYFILE;



sub check{

my $col = shift;

$col = decode_base64($col) if $col =~ m{
            ^
            (?: [A-Za-z0-9+/]{4} )*
            (?:
                [A-Za-z0-9+/]{2} [AEIMQUYcgkosw048] =
            |
                [A-Za-z0-9+/] [AQgw] ==
            )?
            $
        }x;


return $col;
}

__DATA__
A1,A2,A3,A4
B1,B2,B3,B4
1,Just some data,c29tZSBzdHJpbmc=
C1,C2,C3,C4
D1,VGhpcyBpcyBkZWNvZGVkIQ==,D3,D4,GibberishdlkfjsDKjdlslksJAoiasosaSDS
+D==
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