diff --git a/src/index.ts b/src/index.ts
index d7b37c5..6f31054 100644
--- a/src/index.ts
+++ b/src/index.ts
@@ -107,13 +107,12 @@ async function shutdownServer(server: KiCADMcpServer) {
   }
 }
 
-// Run the main function if this file is executed directly
-if (import.meta.url === `file://${process.argv[1]}`) {
-  main().catch((error) => {
-    logger.error(`Unhandled error in main: ${error}`);
-    process.exit(1);
-  });
-}
+// Run the main function - always run when imported as module entry point
+// The import.meta.url check was failing on Windows due to path separators
+main().catch((error) => {
+  console.error(`Unhandled error in main: ${error}`);
+  process.exit(1);
+});
 
 // For testing and programmatic usage
 export { KiCADMcpServer };
diff --git a/src/logger.ts b/src/logger.ts
index d597e12..6a22d8b 100644
--- a/src/logger.ts
+++ b/src/logger.ts
@@ -86,21 +86,10 @@ class Logger {
   private log(level: LogLevel, message: string): void {
     const timestamp = new Date().toISOString();
     const formattedMessage = `[${timestamp}] [${level.toUpperCase()}] ${message}`;
-    
-    // Log to console
-    switch (level) {
-      case 'error':
-        console.error(formattedMessage);
-        break;
-      case 'warn':
-        console.warn(formattedMessage);
-        break;
-      case 'info':
-      case 'debug':
-      default:
-        console.log(formattedMessage);
-        break;
-    }
+
+    // Log to console.error (stderr) only - stdout is reserved for MCP protocol
+    // All log levels go to stderr to avoid corrupting STDIO MCP transport
+    console.error(formattedMessage);
     
     // Log to file
     try {