diff --git a/src/main/kotlin/org/moe/tools/classvalidator/ClassModifier.kt b/src/main/kotlin/org/moe/tools/classvalidator/ClassModifier.kt
new file mode 100644
index 0000000..1bee01b
--- /dev/null
+++ b/src/main/kotlin/org/moe/tools/classvalidator/ClassModifier.kt
@@ -0,0 +1,16 @@
+package org.moe.tools.classvalidator
+
+import org.objectweb.asm.ClassVisitor
+
+/**
+ * A [ClassVisitor] that could modify a class
+ */
+abstract class ClassModifier(api: Int, classVisitor: ClassVisitor?) : ClassVisitor(api, classVisitor) {
+
+    var modified: Boolean = false
+        private set
+
+    fun markAsModified() {
+        modified = true
+    }
+}
diff --git a/src/main/kotlin/org/moe/tools/classvalidator/ClassSaver.kt b/src/main/kotlin/org/moe/tools/classvalidator/ClassSaver.kt
index f4c3ea0..2782ee4 100644
--- a/src/main/kotlin/org/moe/tools/classvalidator/ClassSaver.kt
+++ b/src/main/kotlin/org/moe/tools/classvalidator/ClassSaver.kt
@@ -1,21 +1,32 @@
 package org.moe.tools.classvalidator
 
-import org.moe.common.utils.prepareDir
 import org.objectweb.asm.ClassReader
+import java.nio.file.FileSystems
 import java.nio.file.Files
 import java.nio.file.Path
 
 internal class ClassSaver(
     private val outputDir: Path
 ) {
-    fun save(bytecode: ByteArray?) {
+
+    private val classNameBytecodeMap = mutableMapOf<String, ByteArray>()
+    fun add(bytecode: ByteArray?) {
         if (bytecode == null) {
             return
         }
 
         val cr = ClassReader(bytecode)
-        val outputFile = outputDir.resolve(cr.className + ".class")
-        outputFile.parent.prepareDir()
-        Files.write(outputFile, bytecode)
+        classNameBytecodeMap[cr.className + ".class"] = bytecode
+    }
+
+    fun save() {
+        // In jar replacement
+        val fileSystem = FileSystems.newFileSystem(outputDir, null)
+        fileSystem.use {
+            classNameBytecodeMap.forEach { (fileName, bytecode) ->
+                val outputFile = it.getPath(fileName)
+                Files.write(outputFile, bytecode)
+             }
+        }
     }
 }
diff --git a/src/main/kotlin/org/moe/tools/classvalidator/ClassValidator.kt b/src/main/kotlin/org/moe/tools/classvalidator/ClassValidator.kt
index 4b867a3..7d42667 100644
--- a/src/main/kotlin/org/moe/tools/classvalidator/ClassValidator.kt
+++ b/src/main/kotlin/org/moe/tools/classvalidator/ClassValidator.kt
@@ -1,37 +1,49 @@
 package org.moe.tools.classvalidator
 
-import org.moe.common.utils.classAndJarInputIterator
+import org.moe.common.utils.classpathIterator
 import org.moe.tools.classvalidator.natj.AddMissingAnnotations
 import org.moe.tools.classvalidator.natj.AddMissingNatJRegister
 import org.objectweb.asm.ClassReader
 import org.objectweb.asm.ClassVisitor
 import org.objectweb.asm.ClassWriter
 import java.io.File
-import java.nio.file.Path
 
 object ClassValidator {
     fun process(
-        inputFiles: Set<File>,
-        outputDir: Path,
-        classpath: Set<File>,
+            inputFiles: Set<File>,
+            classpath: Set<File>,
     ) {
-        ContextClassLoaderHolder(
-            ChildFirstClassLoader(classpath.map { it.toURI().toURL() }.toTypedArray())
-        ).use {
-            val classSaver = ClassSaver(outputDir.resolve(OUTPUT_CLASSES))
-
-            inputFiles.classAndJarInputIterator { _, inputStream ->
-                val cr = ClassReader(inputStream)
-
-                val byteCode = processClass(cr) { next ->
-                    next
-                        .let(::AddMissingAnnotations)
-                        .let(::AddMissingNatJRegister)
+        val classSavers = mutableListOf<ClassSaver>()
+        ChildFirstClassLoader(classpath.map { it.toURI().toURL() }.toTypedArray()).use { loader ->
+            ContextClassLoaderHolder(loader).use {
+                inputFiles.forEach { jar ->
+                    val classSaver = ClassSaver(jar.absoluteFile.toPath())
+                    jar.classpathIterator({ _, inputStream ->
+                        val cr = ClassReader(inputStream)
+
+                        val chain = mutableListOf<ClassVisitor>()
+                        fun ClassVisitor.chain(nextBuilder: (ClassVisitor) -> ClassVisitor): ClassVisitor {
+                            val next = nextBuilder(this)
+                            chain.add(next)
+                            return next
+                        }
+
+                        val byteCode = processClass(cr) { next ->
+                            next
+                                    .chain(::AddMissingAnnotations)
+                                    .chain(::AddMissingNatJRegister)
+                        }
+
+                        // Only save modified class
+                        if (chain.any { it is ClassModifier && it.modified }) {
+                            classSaver.add(byteCode)
+                        }
+                    }, { it.endsWith(".class") })
+                    classSavers.add(classSaver)
                 }
-
-                classSaver.save(byteCode)
             }
         }
+        classSavers.forEach { it.save() }
     }
 
     private inline fun processClass(reader: ClassReader, chain: (ClassVisitor) -> ClassVisitor): ByteArray {
@@ -47,6 +59,4 @@ object ClassValidator {
 
         return writer.toByteArray()
     }
-
-    const val OUTPUT_CLASSES = "classes"
 }
diff --git a/src/main/kotlin/org/moe/tools/classvalidator/natj/AddMissingAnnotations.kt b/src/main/kotlin/org/moe/tools/classvalidator/natj/AddMissingAnnotations.kt
index 20581a0..14ecc91 100644
--- a/src/main/kotlin/org/moe/tools/classvalidator/natj/AddMissingAnnotations.kt
+++ b/src/main/kotlin/org/moe/tools/classvalidator/natj/AddMissingAnnotations.kt
@@ -2,6 +2,7 @@ package org.moe.tools.classvalidator.natj
 
 import org.moe.tools.classvalidator.getParentImplementation
 import org.moe.tools.classvalidator.toClass
+import org.moe.tools.classvalidator.ClassModifier
 import org.objectweb.asm.AnnotationVisitor
 import org.objectweb.asm.ClassVisitor
 import org.objectweb.asm.MethodVisitor
@@ -11,7 +12,7 @@ import java.lang.reflect.AnnotatedElement
 
 class AddMissingAnnotations(
     next: ClassVisitor?
-) : ClassVisitor(Opcodes.ASM5, next) {
+) : ClassModifier(Opcodes.ASM5, next) {
     private var skip: Boolean = false
     private var superName: String? = null
     private var interfaces: Array<out String>? = null
@@ -130,6 +131,7 @@ class AddMissingAnnotations(
                         }
                     }
                 }
+                markAsModified()
             }
 
             private fun convertClassToType(value: Any): Any {
diff --git a/src/main/kotlin/org/moe/tools/classvalidator/natj/AddMissingNatJRegister.kt b/src/main/kotlin/org/moe/tools/classvalidator/natj/AddMissingNatJRegister.kt
index c3a892b..145dc63 100644
--- a/src/main/kotlin/org/moe/tools/classvalidator/natj/AddMissingNatJRegister.kt
+++ b/src/main/kotlin/org/moe/tools/classvalidator/natj/AddMissingNatJRegister.kt
@@ -1,5 +1,6 @@
 package org.moe.tools.classvalidator.natj
 
+import org.moe.tools.classvalidator.ClassModifier
 import org.objectweb.asm.AnnotationVisitor
 import org.objectweb.asm.ClassVisitor
 import org.objectweb.asm.MethodVisitor
@@ -13,7 +14,7 @@ import org.objectweb.asm.tree.MethodNode
  */
 class AddMissingNatJRegister(
     next: ClassVisitor?
-) : ClassVisitor(Opcodes.ASM5, next) {
+) : ClassModifier(Opcodes.ASM5, next) {
 
     private var skip: Boolean = false
     private var visit: Boolean = false
@@ -89,6 +90,7 @@ class AddMissingNatJRegister(
                         NatJRuntime.NATJ_OWNER, NatJRuntime.NATJ_REGISTER_NAME,
                         NatJRuntime.NATJ_REGISTER_DESC, false)
                     CLI.accept(mv)
+                    markAsModified()
                     println("Injected NatJ.register() into $name")
                 }
                 NATJREG_LEAVE_ALONE -> {
@@ -107,6 +109,7 @@ class AddMissingNatJRegister(
             mv.visitInsn(Opcodes.RETURN)
             mv.visitMaxs(-1, -1)
             mv.visitEnd()
+            markAsModified()
             println("Injected NatJ.register() into $name")
         }