you need to do "apktool b mms xxx.apk"
replace xxx with whatever name you want for the new apk.
C:\Android\apktool>apktool b mms new.apk
I: Checking whether sources has changed...
I: Checking whether resources has changed...
I: Building resources...
W/asset ( 5676): Asset path C:\Windows\system32\config\systemprofile\apktool\f
ramework\1.apk is neither a directory nor file (type=1).
ERROR: Asset package include 'C:\Windows\system32\config\systemprofile\apktool\f
ramework\1.apk' not found.
Exception in thread "main" brut.androlib.AndrolibException: brut.androlib.Androl
ibException: brut.common.BrutException: could not exec command: [aapt, p, --min-
sdk-version, 16, --target-sdk-version, 16, -F, C:\Users\Henrique\AppData\Local\T
emp\APKTOOL7834780375363419715.tmp, -I, C:\Windows\system32\config\systemprofile
\apktool\framework\1.apk, -S, C:\Android\apktool\mms\res, -M, C:\Android\apktool
\mms\AndroidManifest.xml]
at brut.androlib.Androlib.buildResourcesFull(Androlib.java:358)
at brut.androlib.Androlib.buildResources(Androlib.java:283)
at brut.androlib.Androlib.build(Androlib.java:206)
at brut.androlib.Androlib.build(Androlib.java:176)
at brut.apktool.Main.cmdBuild(Main.java:228)
at brut.apktool.Main.main(Main.java:79)
Caused by: brut.androlib.AndrolibException: brut.common.BrutException: could not
exec command: [aapt, p, --min-sdk-version, 16, --target-sdk-version, 16, -F, C:
\Users\Henrique\AppData\Local\Temp\APKTOOL7834780375363419715.tmp, -I, C:\Window
s\system32\config\systemprofile\apktool\framework\1.apk, -S, C:\Android\apktool\
mms\res, -M, C:\Android\apktool\mms\AndroidManifest.xml]
at brut.androlib.res.AndrolibResources.aaptPackage(AndrolibResources.jav
a:357)
at brut.androlib.Androlib.buildResourcesFull(Androlib.java:336)
... 5 more
Caused by: brut.common.BrutException: could not exec command: [aapt, p, --min-sd
k-version, 16, --target-sdk-version, 16, -F, C:\Users\Henrique\AppData\Local\Tem
p\APKTOOL7834780375363419715.tmp, -I, C:\Windows\system32\config\systemprofile\a
pktool\framework\1.apk, -S, C:\Android\apktool\mms\res, -M, C:\Android\apktool\m
ms\AndroidManifest.xml]
at brut.util.OS.exec(OS.java:89)
at brut.androlib.res.AndrolibResources.aaptPackage(AndrolibResources.jav
a:355)
... 6 more