It can be considered as a sequel to 98724

I adopt the code of ybeltukov (thanks again) and I slightly modify it.

findPoints = Compile[{{n, _Integer}, {low, _Real}, {high, _Real}, {minD, _Real}}, Block[{data = RandomReal[{low, high}, {1, 2}], k = 1, rv, temp}, While[k < n, rv = RandomReal[{low, high}, 2]; temp = Transpose[Transpose[data] - rv]; If[Min[Sqrt[(#.#)] & /@ temp] > minD, data = Join[data, {rv}]; k++;];]; data]]; npts = 150; r = 0.03; minD = 2.2 r; low = 0; high = 1; SeedRandom[159] pts = findPoints[npts, low, high, minD]; g2d = Graphics[{FaceForm@Lighter[Blue, 0.8], EdgeForm@Directive[Thickness[0.004], Black], Disk[#, r] & /@ pts}, PlotRange -> All, Background -> Lighter@Blue] 

mask = BoundaryDiscretizeRegion[#, {{-1, 1}, {-1, 1}}, MaxCellMeasure -> {1 -> .02}] &@ BoundaryDiscretizeRegion[Disk[{0.5, 0.5}, {0.4, 0.5}]]; r2d = DiscretizeGraphics[g2d, MaxCellMeasure -> {1 -> .01}, PlotRange -> All]; inside = RegionIntersection[r2d, mask] 

edge = DiscretizeRegion@*Line@*Intersection @@ Round[{Sort /@ MeshPrimitives[RegionIntersection[r2d, mask], 1][[;; , 1]], Sort /@ MeshPrimitives[RegionDifference[r2d, mask], 1][[;; , 1]]}, .0001]; points = DiscretizeRegion@*Point@*Intersection @@ Round[{MeshPrimitives[RegionDifference[r2d, mask], 0][[;; , 1]], MeshPrimitives[RegionDifference[mask, r2d], 0][[;; , 1]]}, .0001]; regionProduct[reg_, join_: True, y1_: 0, y2_: 1] := Module[{n = MeshCellCount[reg, 0]}, MeshRegion[ Join @@ (ArrayFlatten@{{#[[;; , ;; 1]], #2, #[[;; , 2 ;;]]}} &[ MeshCoordinates@reg, #] & /@ {y1, y2}), {MeshCells[reg, _], MeshCells[reg, _] /. p : {__Integer} :> p + n, If[join, MeshCells[ reg, _] /. {(Polygon | Line)[ p_] :> (Polygon@Join[#, Reverse[#, 2] + n, 2] &@ Partition[p, 2, 1, 1]), Point[p_] :> Line@{p, p + n}}, ## &[]]}]]; mask3d = regionProduct@mask; inside3d = regionProduct[inside, False]; edge3d = regionProduct@edge; points3d = regionProduct@points; toGC[reg_, dim_] := GraphicsComplex[MeshCoordinates@reg, MeshCells[reg, dim]]; Graphics3D[{FaceForm@Lighter[Blue, 0.7], toGC[inside3d, 2], EdgeForm[], toGC[edge3d, 2], toGC[points3d, 1], Lighter@Blue, GeometricTransformation[toGC[mask3d, 2], ScalingTransform[0.999 {1, 1, 1}, RegionCentroid@mask3d]]}, Lighting -> "Neutral", Boxed -> False] 

Graphics3D[{FaceForm@Lighter[Blue, 0.7], toGC[regionProduct[RegionBoundary@inside, False], 1], EdgeForm[], toGC[regionProduct@inside, 2], toGC[edge3d, 2], toGC[points3d, 1], Blue, Opacity[0.11], GeometricTransformation[toGC[mask3d, 2], ScalingTransform[0.999 {1, 1, 1} #, RegionCentroid@mask3d] & /@ Range[0, 1, 0.01]]}, Lighting -> "Neutral", Boxed -> False, BaseStyle -> {RenderingOptions -> {"DepthPeelingLayers" -> 100}}] 

My question is how I can get rid of the disks appeared "cut" and as the result the cylinders appeared also "cut"