diff --git a/tools/export/makefile/__init__.py b/tools/export/makefile/__init__.py
index 959ccafa34..e08e0eae78 100644
--- a/tools/export/makefile/__init__.py
+++ b/tools/export/makefile/__init__.py
@@ -1,6 +1,6 @@
 """
 mbed SDK
-Copyright (c) 2011-2016 ARM Limited
+Copyright (c) 2011-2019 ARM Limited
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
@@ -269,11 +269,10 @@ class Arm(Makefile):
         if self.resources.linker_script:
             sct_file = self.resources.get_file_refs(FileType.LD_SCRIPT)[-1]
             new_script = self.toolchain.correct_scatter_shebang(
-                sct_file.path, join("..", dirname(sct_file.name)))
+                sct_file, dirname(sct_file.name))
             if new_script is not sct_file:
                 self.resources.add_files_to_type(
                     FileType.LD_SCRIPT, [new_script])
-                self.generated_files.append(new_script)
         return super(Arm, self).generate()
 
 class Armc5(Arm):
diff --git a/tools/export/uvision/__init__.py b/tools/export/uvision/__init__.py
index 0011c7dcfe..50404a3d03 100644
--- a/tools/export/uvision/__init__.py
+++ b/tools/export/uvision/__init__.py
@@ -244,12 +244,14 @@ class Uvision(Exporter):
                                       self.resources.inc_dirs),
             'device': DeviceUvision(self.target),
         }
-        sct_name, sct_path = self.resources.get_file_refs(
-            FileType.LD_SCRIPT)[0]
-        ctx['linker_script'] = self.toolchain.correct_scatter_shebang(
-            sct_path, dirname(sct_name))
-        if ctx['linker_script'] != sct_path:
-            self.generated_files.append(ctx['linker_script'])
+        sct_file_ref = self.resources.get_file_refs(FileType.LD_SCRIPT)[0]
+        sct_file_ref = self.toolchain.correct_scatter_shebang(
+            sct_file_ref, dirname(sct_file_ref.name)
+        )
+        self.resources.add_file_ref(
+            FileType.LD_SCRIPT, sct_file_ref.name, sct_file_ref.path
+        )
+        ctx['linker_script'] = sct_file_ref.name
         fpu_included_core_name = ctx['device'].core.replace("-NS", "")
         ctx['cputype'] = fpu_included_core_name.rstrip("FDE")
         if fpu_included_core_name.endswith("FD"):
diff --git a/tools/toolchains/arm.py b/tools/toolchains/arm.py
index 302e47107c..2f7b905d47 100644
--- a/tools/toolchains/arm.py
+++ b/tools/toolchains/arm.py
@@ -1,6 +1,6 @@
 """
 mbed SDK
-Copyright (c) 2011-2013 ARM Limited
+Copyright (c) 2011-2019 ARM Limited
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
@@ -19,7 +19,7 @@ from builtins import str  # noqa: F401
 
 import re
 from copy import copy
-from os.path import join, dirname, splitext, basename, exists, isfile
+from os.path import join, dirname, splitext, basename, exists, isfile, relpath
 from os import makedirs, write, remove
 from tempfile import mkstemp
 from shutil import rmtree
@@ -28,6 +28,7 @@ from distutils.version import LooseVersion
 from tools.targets import CORE_ARCH
 from tools.toolchains.mbed_toolchain import mbedToolchain, TOOLCHAIN_PATHS
 from tools.utils import mkdir, NotSupportedException, run_cmd
+from tools.resources import FileRef
 
 ARMC5_MIGRATION_WARNING = (
     "Warning: We noticed that you are using Arm Compiler 5. "
@@ -272,11 +273,11 @@ class ARM(mbedToolchain):
     def compile_cpp(self, source, object, includes):
         return self.compile(self.cppc, source, object, includes)
 
-    def correct_scatter_shebang(self, scatter_file, cur_dir_name=None):
+    def correct_scatter_shebang(self, sc_fileref, cur_dir_name=None):
         """Correct the shebang at the top of a scatter file.
 
         Positional arguments:
-        scatter_file -- the scatter file to correct
+        sc_fileref -- FileRef object of the scatter file
 
         Keyword arguments:
         cur_dir_name -- the name (not path) of the directory containing the
@@ -288,23 +289,23 @@ class ARM(mbedToolchain):
         Side Effects:
         This method MAY write a new scatter file to disk
         """
-        with open(scatter_file, "r") as input:
+        with open(sc_fileref.path, "r") as input:
             lines = input.readlines()
             if (lines[0].startswith(self.SHEBANG) or
-                    not lines[0].startswith("#!")):
-                return scatter_file
+                not lines[0].startswith("#!")):
+                return sc_fileref
             else:
                 new_scatter = join(self.build_dir, ".link_script.sct")
                 if cur_dir_name is None:
-                    cur_dir_name = dirname(scatter_file)
+                    cur_dir_name = dirname(sc_fileref.path)
                 self.SHEBANG += " -I %s" % cur_dir_name
-                if self.need_update(new_scatter, [scatter_file]):
+                if self.need_update(new_scatter, [sc_fileref.path]):
                     with open(new_scatter, "w") as out:
                         out.write(self.SHEBANG)
                         out.write("\n")
                         out.write("".join(lines[1:]))
 
-                return new_scatter
+                return FileRef(".link_script.sct", new_scatter)
 
     def get_link_command(
             self,
@@ -322,8 +323,9 @@ class ARM(mbedToolchain):
         if lib_dirs:
             args.extend(["--userlibpath", ",".join(lib_dirs)])
         if scatter_file:
-            new_scatter = self.correct_scatter_shebang(scatter_file)
-            args.extend(["--scatter", new_scatter])
+            scatter_name = relpath(scatter_file)
+            new_scatter = self.correct_scatter_shebang(FileRef(scatter_name, scatter_file))
+            args.extend(["--scatter", new_scatter.path])
 
         cmd = self.ld + args