diff --git a/gui/src/aaregui/models/user_sample_model.py b/gui/src/aaregui/models/user_sample_model.py
index c7085c66..71ebd782 100644
--- a/gui/src/aaregui/models/user_sample_model.py
+++ b/gui/src/aaregui/models/user_sample_model.py
@@ -230,9 +230,17 @@ class UserSampleSpreadsheet(QAbstractTableModel):
         self.layoutChanged.emit()
 
     def unique_values_for_column(self, column: int, limit: int = 200) -> list[str]:
+        """Get unique values for a column from currently filtered samples (excluding this column's filter)."""
+        # Get currently filtered samples, but exclude the filter for this column
+        temp_filter = self.__filters.pop(column, None)
+        filtered_samples = self._apply_filter(self.samples)
+        # Restore the filter
+        if temp_filter is not None:
+            self.__filters[column] = temp_filter
+        
         seen: set[str] = set()
         out: list[str] = []
-        for s in self.samples:
+        for s in filtered_samples:
             v = get_entry(s, column)
             if v is None:
                 continue
@@ -244,7 +252,9 @@ class UserSampleSpreadsheet(QAbstractTableModel):
                 out.append(txt)
                 if len(out) >= limit:
                     break
-        if column == 5:
+        
+        # Sort appropriately
+        if column == 5:  # User/pgroup column
             try:
                 out.sort(key=lambda x: int(x[1:]) if x and x[0].lower() == "p" and x[1:].isdigit() else float("inf"))
             except Exception:
@@ -254,9 +264,16 @@ class UserSampleSpreadsheet(QAbstractTableModel):
         return out
 
     def suggested_prefixes_for_sample_name(self, limit: int = 200) -> list[str]:
+        """Get sample name prefixes from currently filtered samples (excluding column 0 filter)."""
+        # Get currently filtered samples, excluding the sample name filter
+        temp_filter = self.__filters.pop(0, None)
+        filtered_samples = self._apply_filter(self.samples)
+        if temp_filter is not None:
+            self.__filters[0] = temp_filter
+        
         rx = re.compile(r"^([A-Za-z]+)")
         counts: dict[str, int] = {}
-        for s in self.samples:
+        for s in filtered_samples:
             name = (s.sample_name or "").strip()
             if not name:
                 continue
@@ -271,9 +288,16 @@ class UserSampleSpreadsheet(QAbstractTableModel):
         return [k for k, _ in items[:limit]]
 
     def suggested_prefixes_for_location(self, limit: int = 200) -> tuple[list[str], list[str]]:
+        """Get location prefixes from currently filtered samples (excluding column 3 filter)."""
+        # Get currently filtered samples, excluding the location filter
+        temp_filter = self.__filters.pop(3, None)
+        filtered_samples = self._apply_filter(self.samples)
+        if temp_filter is not None:
+            self.__filters[3] = temp_filter
+        
         seg_seen: set[str] = set()
         segpos_seen: set[str] = set()
-        for s in self.samples:
+        for s in filtered_samples:
             loc = s.loc_str()  # "-" or like "B3-10"
             if loc and loc != "-" and isinstance(loc, str) and "-" in loc:
                 left = loc.split("-", 1)[0]  # e.g., "B3"