diff --git a/src/call_mode.f90 b/src/call_mode.f90
index f571520..fb187c1 100644
--- a/src/call_mode.f90
+++ b/src/call_mode.f90
@@ -1,4 +1,4 @@
-subroutine call_mode(arg_num,mode)
+subroutine call_mode(arg_pos,mode)
     !This code is used to parse the command line argument for the mode information and calls the required 
     !mode module.
 
@@ -9,16 +9,16 @@ subroutine call_mode(arg_num,mode)
 
     implicit none    
 
-    integer, intent(in) :: arg_num
+    integer, intent(out) :: arg_pos
     character(len=100), intent(in) :: mode
 
     select case(mode)
     case('--create')
-        call create
+        call create(arg_pos)
     case('--convert')
-        call convert   
+        call convert(arg_pos)  
     case('--merge')
-        call merge 
+        call merge(arg_pos) 
     case default
         print *, "Mode ", trim(adjustl(mode)), " currently not accepted. Please check documentation for ", &
                  "accepted modes and rerun."
diff --git a/src/main.f90 b/src/main.f90
index c7ac008..a681d33 100644
--- a/src/main.f90
+++ b/src/main.f90
@@ -17,8 +17,8 @@ program main
     use io
     
 
-    integer ::  arg_num
-    character(len=100) ::  mode
+    integer ::  i, end_mode_arg, arg_num
+    character(len=100) ::  argument
 
     !Call initialization functions
     call lattice_init
@@ -29,13 +29,29 @@ program main
 
     !Determine if a mode is being used and what it is. The first argument has to be the mode
     !if a mode is being used
-    call get_command_argument(1, mode)
+    call get_command_argument(1, argument)
 
-    mode = trim(adjustl(mode))
-    if (mode(1:2) == '--') then 
-        call call_mode(arg_num, mode)
+    argument = trim(adjustl(argument))
+    if (argument(1:2) == '--') then 
+        call call_mode(end_mode_arg, argument)
     end if
 
-    !Finish by writing the files
+    !Now we loop through all of the arguments and check for passed options or for a filename to be written out
+    do i = end_mode_arg-1, arg_num
+        call get_command_argument(i, argument)
+
+        !Check to see if a filename was passed
+        if(scan(argument,'.',.true.) > 0) then 
+            call get_out_file(argument)
+        end if
+    end do
+
+    !Check to make sure a file was passed to be written out and then write out 
+            ! Before building do a check on the file
+    if (outfilenum == 0) then
+        argument = 'none'
+        call get_out_file(argument)
+    end if
     call write_out
+
 end program main
\ No newline at end of file
diff --git a/src/mode_convert.f90 b/src/mode_convert.f90
index d6e1d9b..1f8a6bd 100644
--- a/src/mode_convert.f90
+++ b/src/mode_convert.f90
@@ -8,8 +8,9 @@ module mode_convert
     public 
     contains
 
-    subroutine convert
+    subroutine convert(arg_pos)
         !This subroutine converts a single input file from one format to another
+        integer, intent(out) :: arg_pos
         character(len=100) :: infile, outfile
         real(kind = dp) :: temp_box_bd(6)
         !We have to allocate the element and atom arrays with a size of 1 for the read in code to work
@@ -19,10 +20,7 @@ module mode_convert
         call get_in_file(infile)
         call read_in(1, (/0.0_dp,0.0_dp,0.0_dp/), temp_box_bd)
         call grow_box(temp_box_bd)
-
-        !Now get the outfile, writing is done after all the codes complete
-        call get_command_argument(3, outfile)
-        call get_out_file(outfile)
+        arg_pos = 3
 
     end subroutine convert
 end module mode_convert
\ No newline at end of file
diff --git a/src/mode_create.f90 b/src/mode_create.f90
index 08e201a..23b9100 100644
--- a/src/mode_create.f90
+++ b/src/mode_create.f90
@@ -21,11 +21,12 @@ module mode_create
     public 
     contains
 
-    subroutine create()
+    subroutine create(arg_pos)
         ! Main subroutine which controls execution
 
         character(len=100) :: textholder
-    
+        integer, intent(out) :: arg_pos
+
         integer :: i, ibasis, inod
         real(kind=dp), allocatable :: r_node_temp(:,:,:)
 
@@ -45,14 +46,8 @@ module mode_create
         lat_atom_num = 0
 
         !First we parse the command
-        call parse_command()
+        call parse_command(arg_pos)
 
-        ! Before building do a check on the file
-        if (outfilenum == 0) then
-            textholder = 'none'
-            call get_out_file(textholder)
-        end if
-        
         !Now we setup the unit element and call other init subroutines
         call def_ng_node(1, element_type)
 
@@ -161,10 +156,10 @@ module mode_create
         sub_box_array_bd(2,2,1) = ele_num
     end subroutine create
     !This subroutine parses the command and pulls out information needed for mode_create
-    subroutine parse_command()
+    subroutine parse_command(arg_pos)
 
-
-        integer :: arg_pos, ori_pos, i, j, arglen, stat
+        integer, intent(out) :: arg_pos
+        integer ::  ori_pos, i, j, arglen, stat
         character(len=100) :: textholder
         character(len=8) :: orient_string
 
@@ -245,20 +240,10 @@ module mode_create
                     read(textholder, *) origin(i)
                     arg_pos = arg_pos + 1
                 end do
-            !If a filetype is passed then we add name.ext to the outfiles list
-            case('xyz')
-                textholder = trim(adjustl(name)) //'.xyz'
-                call get_out_file(textholder)
 
             case default
-                !Check to see if it is an option command, if so then mode_create must be finished
-                if(textholder(1:1) == '-') then 
-                    exit
-
-                !Check to see if a filename was passed
-                elseif(scan(textholder,'.',.true.) > 0) then 
-                    call get_out_file(textholder)
-                end if
+                !If it isn't an option then you have to exit
+                exit
             end select
         end do
 
diff --git a/src/mode_merge.f90 b/src/mode_merge.f90
index 0919b70..ca9d068 100644
--- a/src/mode_merge.f90
+++ b/src/mode_merge.f90
@@ -12,13 +12,14 @@ module mode_merge
 
     public 
     contains
-    subroutine merge
+    subroutine merge(arg_pos)
         
+        integer, intent(out) :: arg_pos 
         integer :: i
         real(kind=dp) :: displace(3), temp_box_bd(6)
 
         !First we parse the merge command
-        call parse_command
+        call parse_command(arg_pos)
 
         !Now loop over all files and stack them 
         do i = 1, in_num
@@ -44,10 +45,12 @@ module mode_merge
         return
     end subroutine merge
 
-    subroutine parse_command
+    subroutine parse_command(arg_pos)
+
+        integer, intent(out) :: arg_pos
 
         character(len=100) :: textholder
-        integer :: i, stat, arglen, arg_pos
+        integer :: i, stat, arglen
 
         !Get dimension to concatenate along
         call get_command_argument(2, dim, arglen)
@@ -88,13 +91,8 @@ module mode_merge
             select case(trim(textholder))
 
             case default
-                !Check to see if it is an option command, if so then mode_create must be finished
-                if(textholder(1:1) == '-') then 
-                    exit
-                !Check to see if a filename was passed
-                elseif(scan(textholder,'.',.true.) > 0) then 
-                    call get_out_file(textholder)
-                end if
+                !If it isn't an available option to mode merge then we just exit
+                exit 
             end select
         end do