diff --git a/gui/src/aaregui/panels/file_path_panel.py b/gui/src/aaregui/panels/file_path_panel.py
index b9baa579..a7bc05e4 100644
--- a/gui/src/aaregui/panels/file_path_panel.py
+++ b/gui/src/aaregui/panels/file_path_panel.py
@@ -8,8 +8,11 @@ from aaredaqlib.models import SampleShortInfo
 from aaregui.widgets.title_label import TitleLabel
 
 ## Logic for filenames:
-## 1. Rasters are always placed in raster/ subfolder (managed by DAQ)
-
+## 1. For rasters 'raster/' subfolder is added at the top level of the path (managed by DAQ) - e.g. rasters/20250101/PX-456/01/dataset
+## 2. For screening 'screening/' subfolder is added at the last level of the path (managed by GUI) - e.g. 20250101/PX-456/01/dataset/screening
+## 3. If sample is not registered in the database, it is by default placed in test/<date>
+## 4. If sample is registered in the database and has puck information, it is by default placed in <date>/<puck name>/<puck pos>/
+## 5. If sample is registered in the database as manual, it is by default placed in <date>/manual/<sample name>
 
 class FilePathPanel(QWidget):
     path_updated = Signal(str)
@@ -141,7 +144,7 @@ class FilePathPanel(QWidget):
             self.__puck_pos = sample.pin
             self.run_number_edit.setValue(1)
             if sample.location is not None:
-                self.directory_edit.setText(f"{self.__formatted_date}/{self.__puck_name}/{self.__puck_pos}")
+                self.directory_edit.setText(f"{self.__formatted_date}/{self.__puck_name}/{self.__puck_pos:02d}")
             else:
                 self.directory_edit.setText(f"{self.__formatted_date}/manual/{self.__sample_name}")
             self.update_filename()
diff --git a/gui/src/aaregui/panels/rotation_data_collection.py b/gui/src/aaregui/panels/rotation_data_collection.py
index 04fb0ae5..a5c8695c 100644
--- a/gui/src/aaregui/panels/rotation_data_collection.py
+++ b/gui/src/aaregui/panels/rotation_data_collection.py
@@ -1,3 +1,5 @@
+from pathlib import Path
+
 from PySide6.QtCore import Slot, Signal, Qt
 from PySide6.QtWidgets import QLabel, QComboBox, QPushButton
 
@@ -8,6 +10,11 @@ from aaregui.panels.scan_settings_panel import ScanSettingsPanel
 from aaregui.widgets.number_line_edit import NumberLineEdit
 
 
+def add_screening_to_path(path):
+    p = Path(path)
+    return p.parent / "screening" / p.name
+
+
 class RotationDataCollectionPanel(ScanSettingsPanel):
     rotation_scan = Signal(RotationScanRequest)
 
@@ -97,7 +104,7 @@ class RotationDataCollectionPanel(ScanSettingsPanel):
     def run_screening(self):
         screening_settings = self.screening_type.currentData()
         r = RotationScanRequest(
-            file_prefix=self._filename,
+            file_prefix=str(add_screening_to_path(self._filename)),
             start_omega_deg=self.start_angle.value,
             wedge_omega_deg=self.screening_image_angle.value,
             incr_omega_deg=screening_settings["omega_step_deg"],