diff --git a/importexp b/importexp
index 22468462fbb2f667e967c05e7aa6ee73a79cb88a..e11f980fcd72d54c02daa05a20401b507673f6cb 100755
--- a/importexp
+++ b/importexp
@@ -92,6 +92,7 @@ do
     # 2. get rid of possible +x settings (and optionally -e)
     # 3. to handle external scripts, replace script dir with tmp dir
     # 4. to handle external scripts, replace working dir with tmp dir
+    # 4a to handle external scripts, remove basedir refs from here docs
     # 5. to handle external scripts, replace ./ calls appropriately
     # 6. to handle external scripts, replace build and model dirs appropriately
     # 7. ignore function make_and_change_to_experiment_dir
@@ -136,6 +137,7 @@ cd '$WORK_DIR'
         s:^(\s*)experiments_dir=.*$:\1experiments_dir='$WORK_DIR':
         s:^(\s*)BUILD_DIR=.*$:\1BUILD_DIR='$BUILD_DIR':
         s:^(\s*)EXPDIR=.*$:\1EXPDIR='$WORK_DIR':
+        s:(>\s*)\$\{?basedir\}?/run/:\1:
         s:^(\s*\.\s+)\./:\1'$RUN_BASE_DIR'/:
         s:^(\s*(export\s+)?basedir=).*$:\1'$MODEL_BASE_DIR':
         '${SUBST_BUILD_DIR-}'