diff --git a/src/SelectTree.php b/src/SelectTree.php
index aca66f2..737cece 100644
--- a/src/SelectTree.php
+++ b/src/SelectTree.php
@@ -160,14 +160,29 @@ protected function setUp(): void
 
     protected function buildTree(): Collection
     {
-        // Start with two separate query builders
-        $nullParentQuery = $this->getQuery()->clone()->where($this->getParentAttribute(), $this->getParentNullValue());
-        $nonNullParentQuery = $this->getQuery()->clone()->whereNot($this->getParentAttribute(), $this->getParentNullValue());
-
-        // If we're not at the root level and a modification callback is provided, apply it to null query
+        // If we have a modifyQueryUsing callback, use a single query approach
+        // This handles filtered queries that might not fit the standard null/non-null parent structure
         if ($this->modifyQueryUsing) {
-            $nullParentQuery = $this->evaluate($this->modifyQueryUsing, ['query' => $nullParentQuery]);
+            $query = $this->getQuery()->clone();
+            $query = $this->evaluate($this->modifyQueryUsing, ['query' => $query]);
+            
+            if ($this->withTrashed) {
+                $query->withTrashed($this->withTrashed);
+            }
+            
+            $results = $query->get();
+            
+            // Store results for additional functionality
+            if ($this->storeResults) {
+                $this->results = $results;
+            }
+            
+            return $this->buildTreeFromResults($results);
         }
+        
+        // Original logic for non-filtered queries
+        $nullParentQuery = $this->getQuery()->clone()->where($this->getParentAttribute(), $this->getParentNullValue());
+        $nonNullParentQuery = $this->getQuery()->clone()->whereNot($this->getParentAttribute(), $this->getParentNullValue());
 
         // If we're at the child level and a modification callback is provided, apply it to non null query
         if ($this->modifyChildQueryUsing) {
@@ -223,10 +238,23 @@ private function buildTreeFromResults($results, $parent = null): Collection
 
         // Recursively build the tree starting from the root (null parent)
         $rootResults = $resultMap[$parent] ?? [];
-        foreach ($rootResults as $result) {
-            // Build a node and add it to the tree
-            $node = $this->buildNode($result, $resultMap, $disabledOptions, $hiddenOptions);
-            $tree->push($node);
+        
+        // If we have no root results but we have results, and we're using modifyQueryUsing,
+        // it means the query was filtered and might not have proper root items.
+        // In this case, show all results as root items to prevent empty trees.
+        if (empty($rootResults) && !empty($results) && $this->modifyQueryUsing) {
+            foreach ($results as $result) {
+                // Build a node and add it to the tree
+                $node = $this->buildNode($result, $resultMap, $disabledOptions, $hiddenOptions);
+                $tree->push($node);
+            }
+        } else {
+            // Normal tree building - only show items that are actually root items
+            foreach ($rootResults as $result) {
+                // Build a node and add it to the tree
+                $node = $this->buildNode($result, $resultMap, $disabledOptions, $hiddenOptions);
+                $tree->push($node);
+            }
         }
 
         return $tree;