Emulator

After enabling EFB to RAM, you might need to restart Dolphin. Try using an EFB Scale of 1x also. What are your other graphics settings?

(Metroid Prime 2 also needs "Alpha Pass" to Scan objects (Metroid Prime 1 don´t!))

I see you use R7092, the problem is r7083 messed up Metroid Prime 2´s graphics
and causes scanning issues. See Issue 4060 (Read Migs351`s comment).

I suggest:
Try r7081
Do NOT disable "Destination Alpha Pass"
Use EFB to Ram with EFB Scale of 1x (as Skidau said)

Btw: "I think it was compressed" --> "Pirate"

To: All who commented
I tried all your recommendations but the problem still continues
My graphic settings are:
General settings:
Enhancements - Anisotropic Filtering: 1x
AA:None
Load Native Mipmaps: Checked
EFB Scaled Copy: Checked
The rest of the check boxes in the enhancements section are uncheckd
EFB - Scale: 1x
Enable CPU Access: Checked
Emulate Format Changes: Checked (to RAM)Chache Enabled
Accurate
Texture
Cache - (unchecked)

Advanced Settings
All are unchecked
Please help me fix this problem. thanks! :)

Metroid Prime and Metroid Prime 2 require
enabled "Accurate Texture Cache" set to "fast" !

Reply: nick.lus...@gmx.de
I tried using accurate texture cache and i set it to fast but the problem still lingers

:/ Im not giving up just yet

Check the game properties to make sure you don't have any options enabled in that screen for that game. (Right click the game from the list and choose game properties)

set them all to be "grayed" (Not checked, but also Not UNChecked...)

I played Mp2 with r7124 and Samus´ ship scans fine, no issue.

thanks migs and nick, il try your suggestions as soon as i can.
Nick, what graphic settings did you use for r7124?
Thanks again all of you =)

My settings \ r7124 / Metroid Prime 2
1 http://www.abload.de/img/generalertp.png
2 http://www.abload.de/img/displaycsqf.png
3 http://www.abload.de/img/audio7qub.png
4 http://www.abload.de/img/graphicsgeneralpssj.png
5 http://www.abload.de/img/graphicsadvanced5opf.png
6 http://www.abload.de/img/gameconfigbpzz.png

Result ?

sorry, the results turn out the same.
No matter how much i change up the video settings on dolphin,
there are still certain objects in the game
metroid prime 2 that are not scannable by the
scan visor.
=/

i've got the same issue
i've the pal version,
the ntsc version is fixed (!)

you must enable accurate texture cache to fast
copy efb to ram, and desired scale. ;)

Randay and k95, please list your CPU specs.

i3-330m intel hd graphics

a little late xd

I made it work.
I installed the ubuntu OS on my pc and run dolphin through there. Metroid prime seems to work fine.