One thing is for sure. EMM386 does not display startup menu, because it is loading after menu is displayed.

OK.

Correction in my question. What i mean to say is not removing the entire startup menu, but to remove the heading that says "Microsoft windows 98 startup ...". My aim is to remove the file that causes this heading and use any other freeware file that does not cause this heading and at the same time does not modify the working of the disk.

I'm not quite sure, but look in CONFIG.SYS file. If there is [MENU] section system will display this menu.

Could you post more about this menu. What options are displayed in it. Because there is another menu wchich offers to bypass startup files.

Posting the entire Config.sys file of Bart's bootable floppy disk image i had created:

[menu]
menuitem=AUTO, Boot with emm386 (most compatible)
menuitem=MAX, Boot with emm386 (max memory)
menuitem=NOEMM, Boot without emm386
menuitem=CLEAN, Clean boot
menudefault=AUTO,30

[AUTO]
switches=/f
break=off
dos=high,umb
files=20
buffers=20
lastdrive=z
device=\bin\himem.sys /testmem:off /v
device=\bin\emm386.exe /v x=d000-d8ff h=128 noems notr
shell=\command.com /e:1024 /p
devicehigh=\bin\ifshlp.sys

[MAX]
switches=/f
break=off
dos=high,umb
files=20
buffers=20
lastdrive=z
device=\bin\himem.sys /testmem:off /v
device=\bin\emm386.exe /v h=128 noems
shell=\command.com /e:1024 /p
devicehigh=\bin\ifshlp.sys

[NOEMM]
switches=/f
break=off
dos=high,umb
files=20
buffers=20
lastdrive=z
device=\bin\himem.sys /testmem:off /v
shell=\command.com /e:1024 /p
device=\bin\ifshlp.sys

[CLEAN]
shell=\command.com /p

All is clear now. Boot disk is made of microsoft windows 98. Menu is diplayed by IO.SYS itself, because menu is defined in Config.sys. If you remove [MENU] section, menu will not be displayed.
If You don't need the menu, delete all sections except the one you need.
Some Autoexec.bat changes will be necesary also.

OK.
I need the menu, but not the heading that says "Microsoft windows 98...".

How do i do that ? What changes are to be made?

Is there any free alternative file to this IO.SYS which does not display these type of headings like Miicrosoft ? and which i can use along with the existing files without making any changes to the structure of the boot disk?

Thank you.

This is quite a problem. IO.SYS is a core of Windows 98 DOS mode. So using other IO.SYS means using other DOS version.

I see two possibilities.
First, a direct modification of IO.SYS with a hex editor.
Second, finding another DOS compatible system capable of using startup menu.

Maybe Free DOS will do, but I don't remember if it is capable of using boot menu. I will have to check it. I did not played with the newest version, yet.