diff --git a/.travis/install.cppcheck b/.travis/install.cppcheck
index 2880723e24c126dc626472abed9acdaefb06284a..767c23608e0f9cb1ae22482163b880293fb329d5 100755
--- a/.travis/install.cppcheck
+++ b/.travis/install.cppcheck
@@ -3,7 +3,7 @@
 set -e
 set -x
 
-cd "$(mktemp -d)"
+cd "$(mktemp -dt plumed.XXXXXX)"
 
 git clone https://github.com/danmar/cppcheck.git
 cd cppcheck
diff --git a/.travis/install.doxygen b/.travis/install.doxygen
index 1f020a22e0a5d7e0aa9b17b68fac69811c4642e1..f62bda74d2d24ca4df78e124f68ebfe6add9ef92 100755
--- a/.travis/install.doxygen
+++ b/.travis/install.doxygen
@@ -3,7 +3,7 @@
 set -e
 set -x
 
-cd "$(mktemp -d)"
+cd "$(mktemp -dt plumed.XXXXXX)"
 
 git clone https://github.com/doxygen/doxygen.git
 
diff --git a/.travis/install.gawk b/.travis/install.gawk
index d7fdf6edf2ff42d8ce8ab37c6564d9a8e0064d45..d2eb4386684073ec3ced26d1640f1da84d119edd 100755
--- a/.travis/install.gawk
+++ b/.travis/install.gawk
@@ -3,7 +3,7 @@
 set -e
 set -x
 
-cd "$(mktemp -d)"
+cd "$(mktemp -dt plumed.XXXXXX)"
 
 version=4.1.4
 
diff --git a/.travis/install.lcov b/.travis/install.lcov
index dc38f3a2583867a1a2cb8655100d82f4a9d90906..4df4f61b815e11116952e834ab94dcf8497f8270 100755
--- a/.travis/install.lcov
+++ b/.travis/install.lcov
@@ -3,7 +3,7 @@
 set -e
 set -x
 
-cd "$(mktemp -d)"
+cd "$(mktemp -dt plumed.XXXXXX)"
 
 git clone https://github.com/linux-test-project/lcov.git
 
diff --git a/.travis/install.xdrfile b/.travis/install.xdrfile
index 296a8eaf3d1bb363dd05987c077b16d2af7f36ee..e30bb5a312f9b3088f660a7f5036b0504f21dc98 100755
--- a/.travis/install.xdrfile
+++ b/.travis/install.xdrfile
@@ -3,7 +3,7 @@
 set -e
 set -x
 
-cd "$(mktemp -d)"
+cd "$(mktemp -dt plumed.XXXXXX)"
 
 echo "installing xdrfile library"
 # wget ftp://ftp.gromacs.org/pub/contrib/xdrfile-1.1.4.tar.gz
diff --git a/regtest/scripts/check b/regtest/scripts/check
index 7d35f64e86ef5be76bf5097b25cdae4288ba8c17..3d9360bf70e1fbfea626d265e84d4a418038ec3f 100755
--- a/regtest/scripts/check
+++ b/regtest/scripts/check
@@ -30,8 +30,8 @@ dirs=$(
   done
 )
 
-file1=$(mktemp)
-file2=$(mktemp)
+file1=$(mktemp -t plumed.XXXXXX)
+file2=$(mktemp -t plumed.XXXXXX)
 
 for dir in $dirs
 do
diff --git a/src/maketools/codecheck b/src/maketools/codecheck
index 4c59c8349bb8cf24a6998d4db4f84fcb0541c059..04db28d03920c8d7f9f980670630ba203faed513 100755
--- a/src/maketools/codecheck
+++ b/src/maketools/codecheck
@@ -52,7 +52,7 @@ fi
 # done
 # echo "+++++++++++++++++++++++++++++++++++++"
 
-TMPDIR="$(mktemp -d)"
+TMPDIR="$(mktemp -dt plumed.XXXXXX)"
 FATAL_FILE="$TMPDIR/codecheck.fatal"
 CLEAN_FILE="$TMPDIR/codecheck.clean"
 
diff --git a/src/maketools/plumedcheck b/src/maketools/plumedcheck
index 9f0b038cbf1214744f37e3340f802ce8a84b5733..6d442b6b5fb7de3f8369a50777655e4fbff3776b 100755
--- a/src/maketools/plumedcheck
+++ b/src/maketools/plumedcheck
@@ -14,7 +14,7 @@
 # DOC: In case you think you have a valid reason for a code not passing the check
 # DOC: to be merged, please contact the developers.
 
-TEMP=$(mktemp)
+TEMP=$(mktemp -t plumed.XXXXXX)
 
 cat > $TEMP << \EOF
 
@@ -144,7 +144,7 @@ BEGIN{
   core_modules["reference"]=1
 
 # create tmp dir for future usage
-  "mktemp -d" | getline tmpdir
+  "mktemp -dt plumed.XXXXXX" | getline tmpdir
 }
 
 # for each input file