Delete all Slack files. Usage: python slack_delete.py --token <your token>

slack_delete.py

import argparse
import requests
import time
import json


def main():
    """
    Entry point of the application
    :return: void
    """
    parser = argparse.ArgumentParser()
    parser.add_argument("-t", "--token", required=True, help="Specifies the OAuth token used for authentication, created at (https://api.slack.com/docs/oauth-test-tokens)")
    parser.add_argument("-d", "--days", type=int, default=None, help="Delete files older than x days (optional)")
    parser.add_argument("-c", "--count", type=int, default=1000, help="Max amount of files to delete at once (optional)")
    options = parser.parse_args()

    try:
        print "[*] Fetching file list.."
        file_ids = list_file_ids(token=options.token, count=options.count, days=options.days)

        print "[*] Deleting files.."
        delete_files(token=options.token, file_ids=file_ids)

        print "[*] Done"

    except KeyboardInterrupt:
        print "\b\b[-] Aborted"
        exit(1)


def calculate_days(days):
    """
    Calculate days to unix time
    :param days: int
    :return: int
    """
    return int(time.time()) - days * 24 * 60 * 60


def list_file_ids(token, count, days=None):
    """
    Get a list of all file id's
    :param token: string
    :param count: int
    :param days: int
    :return: list
    """
    if days:
        params = {'token': token, 'count': count, 'ts_to': calculate_days(days)}
    else:
        params = {'token': token, 'count': count}

    uri = 'https://slack.com/api/files.list'
    response = requests.get(uri, params=params)
    files = json.loads(response.text)['files']
    return [f['id'] for f in files]


def delete_files(token, file_ids):
    """
    Delete a list of files by id
    :param token: string
    :param file_ids: list
    :return: void
    """
    count = 0
    num_files = len(file_ids)
    for file_id in file_ids:
        count += 1
        params = {'token': token, 'file': file_id}
        uri = 'https://slack.com/api/files.delete'
        response = json.loads(requests.get(uri, params=params).text)
        if response["ok"]:
            print "[+] Deleted", count, "of", num_files, "-", file_id, json.loads(response.text)['ok']
        else:
            print "[!] Unable to delete", count, "of", num_files, "-", file_id + ", reason:", response["error"]

if __name__ == '__main__':
    main()

Forked to preserve pinned and starred files. Thanks to @Paradoxis @jackcarter @jamescmartinez for sharing!

follow @notz advice. Worked ok.

How to we delete bot users files, a files uploaded using bot users api Token, currently this says

u'{"ok":false,"error":"not_allowed_token_type"}'

For the guys who do not want to code, the easier way to delete and back-up slack files in bulk is using
https://delete-slack-files.com/

Good luck!