1/ Does anyone knows how to fill the space just like the reference ? :
i tried to scale the edge but everytime it goes beyond the paper :
2/ Is there anyway to make the paper just like the reference so the cupcake would appear through it ?
The most common way is to shape the bottom of the cupcake like a cup, or to delete the invisible part and adjust it properly
Or you can cover the space by inflating the edges of the cupcake down 
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if it was me i will create a vertex group containing the area that is meant to be inside the cup.
add a shrinkwrap modifier on the cake to the cup. that only affect that vertex group. play with the options (project maybe your friend). after that you can apply modifier and tweak in sculpt mode if need.
while the modifier is still on you can tweak the cup and the cake will follow. if you want more crease in sculpt mode
cake kinda showing through the paper, better be done in the materials. mix two materials with a shader mix driven by a map or pointiness (to get the creases of the cup) or you can paint it yourself. one material for paper and the other similar to the cake.
and try to plug that same map that mix from paper to cake to a slight bump. cause in reality that’s cake Material that poured through the paper
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In my opinion you should model whole cupcake. The bottom part as well. And than apply the paper cover with f.ex. shrink modifier.
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Yes but this is rather simple geometry. It’s simpler than the paper cover geometry so this is the reason that this edge goes through the paper covering. When you make bottom of the cupcake as complicated as cupcake surface is and than shrink warp the paper cover the effect should be better. Now the paper covering has much more detailed geometry than the cupcake itself.
But I agree with you that the seethrough paper could be done by creating a good material.
but when i shrink wrap the paper on the cake, i’'ll lose details, the paper would be flat,the waves on the cup would be gone, and what happens when i make the bottom of the cupcake more complicated ?
@Blendit that why i suggested the opposite… to shrink wrap the bottom of the cake to the paper. (i called the paper cup in first reply ) cause i saw the details 
. now because you don’t want the whole cake to shrink wrap i suggested you create a vertex group for the bottom of the cake that is inside the paper
the shrinkwrap will be added on the cake and the target is the cup/paper and you select that vertex group in the modifier options so it affects just the bottom
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Why do you not use cloth for the cake and activate the pressure option ? This will make the cake grow from inside the paper cup.
You will need to animate the strength of the pressure to control the amount of growth.
honestly, i don’t know how to do this can you give me some resources or a youtube video to learn it ?.cuz it seems a briliant idea to not lose the details.
you mean cloth in sculpting ? explain more i’m a newbie in blender 
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@Blendit
sorry for the awesome cake i just made (not for sale lol)
made it smaller than the cup for illustration purpose the closer to the target shape the better shrink wrap will work btw
and if you keep the shrinkwrap modifier live (not apply it) make changes to the paper cup will make the cake follow
you can apply the modifier and tweak the cake in sculpt mode (ex: if you don’t want to to stick at the top some smooth there )
please note the limit in the shrinkwrap modifier. if it’s 0 it means no limit, so blender will try to move your vertices to a position on the target whatever it takes. giving a limit is telling blender shrinkwrap if the target is at a certain distance only
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No - I mean cloth in place of sculpting. You can make the cake grow and as it is cloth it will deform around other objects. You need to add collision modifier to the paper cup. You hit play and watch the cake grow to its final shape…
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what do you mean by cloth ?
it looks to me like you did the opposite.
paper =>shrinkwrap => cake
apply the shrinkpwrap on the cake and select the paper as target
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Cloth Modifier.
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it worked, thnx 
what about the semi-transparant paper ?
my please!
look at this thread it will inspire you a lot :
I think using the translucent BSDF/ or the subsurface of the principled BSDF will help with that:
even tho there is a space where the paper sticks out, feels like a thicker paper too than yours and stayed clean from the outside
based on your model and reference, you have no space but still i will give subsurface a try, and the paper in your reference looks like it have more permeability and cake material went through.
maybe a mix shader between paper material and cake material driven by a map that you paint that noise/dots where the cake passed thorough the paper and using it to to drive also a bump/displacement (adding pointiness to mix can help to emphasis the effect based on the paper folds)
a quick tutorial about mixing shaders:
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