diff --git a/lib/spack/spack/mixins.py b/lib/spack/spack/mixins.py
index 82e6f8bdad..0a43e76961 100644
--- a/lib/spack/spack/mixins.py
+++ b/lib/spack/spack/mixins.py
@@ -143,24 +143,47 @@ def filter_compiler_wrappers(*files, **kwargs):
     whatever compiler they were built with.
 
     Args:
-        *files: files to be filtered
-        **kwargs: at present supports the keyword 'after' to specify after
-            which phase the files should be filtered (defaults to 'install').
+        *files: files to be filtered relative to the search root (which is,
+            by default, the installation prefix)
+
+        **kwargs: allowed keyword arguments
+
+            after
+                specifies after which phase the files should be
+                filtered (defaults to 'install')
+
+            relative_root
+                path relative to prefix where to start searching for
+                the files to be filtered. If not set the install prefix
+                wil be used as the search root. **It is highly recommended
+                to set this, as searching from the installation prefix may
+                affect performance severely in some cases**.
+
+            ignore_absent, backup
+                these two keyword arguments, if present, will be forwarded
+                to ``filter_file`` (see its documentation for more information
+                on their behavior)
     """
     after = kwargs.get('after', 'install')
+    relative_root = kwargs.get('relative_root', None)
+
+    filter_kwargs = {
+        'ignore_absent': kwargs.get('ignore_absent', True),
+        'backup': kwargs.get('backup', False),
+        'string': True
+    }
 
     def _filter_compiler_wrappers_impl(self):
+        # Compute the absolute path of the search root
+        root = os.path.join(
+            self.prefix, relative_root
+        ) if relative_root else self.prefix
+
         # Compute the absolute path of the files to be filtered and
         # remove links from the list.
-        abs_files = llnl.util.filesystem.find(self.prefix, files)
+        abs_files = llnl.util.filesystem.find(root, files)
         abs_files = [x for x in abs_files if not os.path.islink(x)]
 
-        filter_kwargs = {
-            'ignore_absent': True,
-            'backup': False,
-            'string': True
-        }
-
         x = llnl.util.filesystem.FileFilter(*abs_files)
 
         x.filter(os.environ['CC'], self.compiler.cc, **filter_kwargs)
diff --git a/var/spack/repos/builtin/packages/hdf5/package.py b/var/spack/repos/builtin/packages/hdf5/package.py
index 3c729412ab..0ead42d41b 100644
--- a/var/spack/repos/builtin/packages/hdf5/package.py
+++ b/var/spack/repos/builtin/packages/hdf5/package.py
@@ -97,7 +97,7 @@ class Hdf5(AutotoolsPackage):
     patch('h5f90global-mult-obj-same-equivalence-same-common-block.patch',
           when='@1.10.1%intel@18')
 
-    filter_compiler_wrappers('h5cc', 'h5c++', 'h5fc')
+    filter_compiler_wrappers('h5cc', 'h5c++', 'h5fc', relative_root='bin')
 
     def url_for_version(self, version):
         url = "https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-{0}/hdf5-{1}/src/hdf5-{1}.tar.gz"
diff --git a/var/spack/repos/builtin/packages/mpich/package.py b/var/spack/repos/builtin/packages/mpich/package.py
index 69dd75e3e1..5573b71197 100644
--- a/var/spack/repos/builtin/packages/mpich/package.py
+++ b/var/spack/repos/builtin/packages/mpich/package.py
@@ -71,7 +71,9 @@ class Mpich(AutotoolsPackage):
     provides('mpi@:3.0', when='@3:')
     provides('mpi@:1.3', when='@1:')
 
-    filter_compiler_wrappers('mpicc', 'mpicxx', 'mpif77', 'mpif90')
+    filter_compiler_wrappers(
+        'mpicc', 'mpicxx', 'mpif77', 'mpif90', 'mpifort', relative_root='bin'
+    )
 
     # fix MPI_Barrier segmentation fault
     # see https://lists.mpich.org/pipermail/discuss/2016-May/004764.html
diff --git a/var/spack/repos/builtin/packages/mvapich2/package.py b/var/spack/repos/builtin/packages/mvapich2/package.py
index 256418da9c..8dab2e9d6d 100644
--- a/var/spack/repos/builtin/packages/mvapich2/package.py
+++ b/var/spack/repos/builtin/packages/mvapich2/package.py
@@ -107,7 +107,9 @@ class Mvapich2(AutotoolsPackage):
     depends_on('libpciaccess', when=(sys.platform != 'darwin'))
     depends_on('cuda', when='+cuda')
 
-    filter_compiler_wrappers('mpicc', 'mpicxx', 'mpif77', 'mpif90', 'mpifort')
+    filter_compiler_wrappers(
+        'mpicc', 'mpicxx', 'mpif77', 'mpif90', 'mpifort', relative_root='bin'
+    )
 
     def url_for_version(self, version):
         base_url = "http://mvapich.cse.ohio-state.edu/download"
diff --git a/var/spack/repos/builtin/packages/openmpi/package.py b/var/spack/repos/builtin/packages/openmpi/package.py
index 343b69ea7e..889455aae0 100644
--- a/var/spack/repos/builtin/packages/openmpi/package.py
+++ b/var/spack/repos/builtin/packages/openmpi/package.py
@@ -228,7 +228,8 @@ class Openmpi(AutotoolsPackage):
         'mpif90-vt-wrapper-data.txt',
         'mpif90-wrapper-data.txt',
         'mpif77-vt-wrapper-data.txt',
-        'mpif77-wrapper-data.txt'
+        'mpif77-wrapper-data.txt',
+        relative_root=os.path.join('share', 'openmpi')
     )
 
     def url_for_version(self, version):
diff --git a/var/spack/repos/builtin/packages/r/package.py b/var/spack/repos/builtin/packages/r/package.py
index cb955579a3..4b5dd05c33 100644
--- a/var/spack/repos/builtin/packages/r/package.py
+++ b/var/spack/repos/builtin/packages/r/package.py
@@ -88,7 +88,9 @@ class R(AutotoolsPackage):
 
     patch('zlib.patch', when='@:3.3.2')
 
-    filter_compiler_wrappers('Makeconf')
+    filter_compiler_wrappers(
+        'Makeconf', relative_root=os.path.join('rlib', 'R', 'etc')
+    )
 
     @property
     def etcdir(self):