diff --git a/CHANGES.rst b/CHANGES.rst
index 83cd8633de..e2c387e131 100644
--- a/CHANGES.rst
+++ b/CHANGES.rst
@@ -14,6 +14,11 @@ linelists.cdms
 - Add whole catalog retrieval, improve error messaging for unparseable lines,
   improve metadata catalog, and improve lookuptable behavior [#3173,#2901]
 
+heasarc
+^^^^^^^
+
+- Fix Heasarc.download_data for Sciserver. [#3183]
+
 jplspec
 ^^^^^^^
 
@@ -69,7 +74,6 @@ Infrastructure, Utility and Other Changes and Additions
 -------------------------------------------------------
 
 
-
 0.4.8 (2025-01-16)
 ==================
 
diff --git a/astroquery/heasarc/core.py b/astroquery/heasarc/core.py
index a7229f4c1c..04986f6fb1 100644
--- a/astroquery/heasarc/core.py
+++ b/astroquery/heasarc/core.py
@@ -692,16 +692,17 @@ def _copy_sciserver(self, links, location='.'):
         Users should be using `~self.download_data` instead
 
         """
-        if not (os.path.exists('/FTP/') and os.environ['HOME'].split('/')[-1] == 'idies'):
+        if not os.path.exists('/FTP/'):
             raise FileNotFoundError(
                 'No data archive found. This should be run on Sciserver '
                 'with the data drive mounted.'
             )
 
-        if not os.path.exists(location):
-            os.mkdir(location)
+        # make sure the output folder exits
+        os.makedirs(location, exist_ok=True)
 
         for link in links['sciserver']:
+            link = str(link)
             log.info(f'Copying to {link} from the data drive ...')
             if not os.path.exists(link):
                 raise ValueError(
@@ -711,7 +712,8 @@ def _copy_sciserver(self, links, location='.'):
                     'Heasarc Help desk'
                 )
             if os.path.isdir(link):
-                shutil.copytree(link, location)
+                download_dir = os.path.basename(link.strip('/'))
+                shutil.copytree(link, f'{location}/{download_dir}')
             else:
                 shutil.copy(link, location)
 
diff --git a/astroquery/heasarc/tests/test_heasarc.py b/astroquery/heasarc/tests/test_heasarc.py
index 47cd7ddc14..1c63da8c8d 100644
--- a/astroquery/heasarc/tests/test_heasarc.py
+++ b/astroquery/heasarc/tests/test_heasarc.py
@@ -1,8 +1,8 @@
 # Licensed under a 3-clause BSD style license - see LICENSE.rst
 
 import os
-import shutil
 import pytest
+import tempfile
 from unittest.mock import patch, PropertyMock
 from astropy.coordinates import SkyCoord
 from astropy.table import Table
@@ -304,6 +304,24 @@ def test_download_data__missingcolumn(host):
         Heasarc.download_data(Table({"id": [1]}), host=host)
 
 
+def test_download_data__sciserver():
+    with tempfile.TemporaryDirectory() as tmpdir:
+        datadir = f'{tmpdir}/data'
+        downloaddir = f'{tmpdir}/download'
+        os.makedirs(datadir, exist_ok=True)
+        with open(f'{datadir}/file.txt', 'w') as fp:
+            fp.write('data')
+        # include both a file and a directory
+        tab = Table({'sciserver': [f'{tmpdir}/data/file.txt', f'{tmpdir}/data']})
+        # The patch is to avoid the test that we are on sciserver
+        with patch('os.path.exists') as exists:
+            exists.return_value = True
+            Heasarc.download_data(tab, host="sciserver", location=downloaddir)
+        assert os.path.exists(f'{downloaddir}/file.txt')
+        assert os.path.exists(f'{downloaddir}/data')
+        assert os.path.exists(f'{downloaddir}/data/file.txt')
+
+
 def test_download_data__outside_sciserver():
     with pytest.raises(
         FileNotFoundError,
@@ -350,10 +368,10 @@ def test_s3_mock_basic(s3_mock):
 def test_s3_mock_file(s3_mock):
     links = Table({"aws": [f"s3://{s3_bucket}/{s3_key1}"]})
     Heasarc.enable_cloud(profile=False)
-    Heasarc.download_data(links, host="aws", location=".")
-    file = s3_key1.split("/")[-1]
-    assert os.path.exists(file)
-    os.remove(file)
+    with tempfile.TemporaryDirectory() as tmpdir:
+        Heasarc.download_data(links, host="aws", location=tmpdir)
+        file = s3_key1.split("/")[-1]
+        assert os.path.exists(f'{tmpdir}/{file}')
 
 
 @pytest.mark.filterwarnings("ignore::DeprecationWarning")
@@ -361,9 +379,9 @@ def test_s3_mock_file(s3_mock):
 def test_s3_mock_directory(s3_mock):
     links = Table({"aws": [f"s3://{s3_bucket}/{s3_dir}"]})
     Heasarc.enable_cloud(profile=False)
-    Heasarc.download_data(links, host="aws", location=".")
-    assert os.path.exists("location")
-    assert os.path.exists("location/file1.txt")
-    assert os.path.exists("location/sub/file2.txt")
-    assert os.path.exists("location/sub/sub2/file3.txt")
-    shutil.rmtree("location")
+    with tempfile.TemporaryDirectory() as tmpdir:
+        Heasarc.download_data(links, host="aws", location=tmpdir)
+        assert os.path.exists(f"{tmpdir}/location")
+        assert os.path.exists(f"{tmpdir}/location/file1.txt")
+        assert os.path.exists(f"{tmpdir}/location/sub/file2.txt")
+        assert os.path.exists(f"{tmpdir}/location/sub/sub2/file3.txt")