diff --git a/src/main/java/org/whitesource/agent/utils/FilesScanner.java b/src/main/java/org/whitesource/agent/utils/FilesScanner.java
index b4b6f1b..29b4c18 100644
--- a/src/main/java/org/whitesource/agent/utils/FilesScanner.java
+++ b/src/main/java/org/whitesource/agent/utils/FilesScanner.java
@@ -126,7 +126,7 @@ private Map<String, Set<String>> getTopFoldersWithIncludedFiles(String rootFolde
                     Path folderPath = Paths.get(folder);
                     boolean shouldRemove = false;
                     try {
-                        shouldRemove = otherFolderPath.toFile().getCanonicalPath().startsWith(folderPath.toFile().getCanonicalPath());
+                        shouldRemove = otherFolderPath.toFile().getCanonicalFile().toPath().startsWith(folderPath.toFile().getCanonicalFile().toPath());
                     } catch (Exception e) {
                         logger.debug("could not get file path " + otherFolderPath + folderPath, e.getStackTrace());
                         logger.warn("could not get file path " + otherFolderPath + folderPath, e.getMessage());
@@ -152,4 +152,4 @@ public boolean isIncluded(File file, String[] includes, String[] excludes, boole
         scanner.setCaseSensitive(globCaseSensitive);
         return scanner.isIncluded(file);
     }
-}
\ No newline at end of file
+}